bluuebunny/crossref_metadata_2025 huggingface dataset:
Different habitats of ferns growing in the Amonkoton stream, Zerafshan Valley, Uzbekistan
Authors: MUMINOV DILSHODJON , KHAYDAROV KHISLAT , ZHALOV KHOLMUROD , HASANOV MURTOZA , ABDUMUMINOVA RANO , OCHILOV ULUGBEK
Published: August 2024

Abstract. Muminov D, Khaydarov K, Zhalov K, Hasanov M, Abdumuminova R, Ochilov U. 2024. Different habitats of ferns growing in the Amonkoton Stream (Zerafshan Valley), Uzbekistan. Biodiversitas 25: 2696-2704. The Zerafshan Valley, Uzbekistan, characterized by a warm and arid climate, has declined vegetation and soil quality over recent decades, marking a stark departure from its once lush past. Understanding the nuanced relationship between species and their habitat is imperative to unraveling this ecological transformation. This research delves into ferns, which are highly responsive to environmental factors, seeking to elucidate their circumstances within the changing ecosystem. Through strategically planned intensive transects and plots as proxies for fern growth and habitat analysis, statistical methods like the Shannon-Wiener Index (H) and Bray-Curtis index were deployed. The climate-related information analysis was conducted using the CRU TS 4.07 tool. We made use of average temperatures and precipitation over 120 years. The results of analyses have been acquired from 490 fern individuals belonging to 13 species, 7 genera, and 6 families. There are four species: Equisetum arvense L., Equisetum ramosissimum Desf., Cystopteris fragilis (L.) Bernh. and Adiantum capillus-veneris L. were employed as indicators of habitat. The findings underscore a substantial decline in fern-populated areas, resulting in diminished diversity and abundance and a relatively high rarity level. Furthermore, a latitudinal correlation with ferns along the stream direction is exhibited by four indicator species, offering valuable insights into the intricate dynamics of the Zerafshan Valley's ecosystem.
Structure and composition of mangrove vegetation in the coastal area of Mandalika International Street Circuit, Central Lombok, Indonesia
Authors: JAYADI EDI MUHAMAD , RAHMAN FIRMAN ALI , IHSAN MUHAMMAD SHOHIBUL , FITRIAH LENY , AGUSTINI DWI
Published: August 2024

Abstract. Jayadi EM, Rahman FA, Ihsan MS, Fitriah L, Agustini D. 2024. Structure and composition of mangrove vegetation in the coastal area of Mandalika International Street Circuit, Central Lombok, Indonesia. Biodiversitas 25: 2719-2728. Mangrove is one of the coastal vegetation that has an ecological role as a buffer for essential areas such as the Mandalika International Street Circuit Special Economic Zone located around the coastal area of Central Lombok District, West Nusa Tenggara, Indonesia. This research, conducted with a rigorous methodology, aims to determine the current condition of the diversity of mangrove vegetation and their vegetation structure as a buffer ecosystem in the Mandalika International Street Circuit area, West Nusa Tenggara. The study utilized the quadrant transect method, a widely accepted approach, with plots measuring 2×2 m2 (seedling strata), 5×5 m2 (sapling strata), 10×10 m2 (pole strata), and 20×20 m2 (tree strata). The total number of observation plots was 49 measuring plots in a total area of the mangrove ecosystem of 38.68 ha. The research results showed that four families and five genera were found consisting of 11 species of mangroves: Avicennia alba Blume, Avicennia lanata Ridl., Avicennia marina (Forssk.) Vierh., Ceriops tagal (Perr.) C.B.Rob., Rhizophora apiculata Blume, Rhizophora mucronata Lam., Rhizophora stylosa Griffith, Scyphiphora hydrophyllaceae C.F.Gaertn., Sonneratia alba Sm., Sonneratia caseolaris (L.) Engl., and Sonneratia ovata Backer. Rhizophora apiculata is the species with the highest density in the strata of seedlings (261 individuals/ha), saplings (312 individuals/ha), poles (444 individuals/ha), and trees (160 individuals/ha); this condition is in line with the importance value index R. apiculata with the highest values in seedlings (105.21%), saplings (89.14%), poles (129.61%), and trees (119.60%). Shannon-Wiener diversity index in the mangrove ecosystem in the Mandalika International Street Circuit is in the quite good category with an even diversity value with an H' value of no less than 1 (1.425).
Papel das redes sociais na melhoria de políticas públicas de inclusão no ensino superior: um breve estudo sobre o engajamento e as opiniões dos usuários no Twitter
Authors: França George , Junior Alvez Fábio , Pereira Filha Maria do S
Published: August 2024

Este estudo analisa o potencial das redes sociais para o aprimoramento de políticas públicas de inclusão no ensino superior brasileiro, a partir de postagens no Twitter sobre o Sistema de Seleção Unificada (Sisu), ação do Ministério da Educação (MEC). A análise dos dados, coletados durante os primeiros dias de inscrição no processo seletivo do Sisu do primeiro semestre de 2023, demonstra a relevância do tema no Twitter e o amplo engajamento que ele enseja para além do território nacional. No Brasil, diferentes regiões são representadas nas interações de usuários sobre o Sisu, com destaque para estados como Rio de Janeiro, São Paulo e Minas Gerais. As palavras mais utilizadas foram quantificadas com o objetivo de identificar o contexto das ideias centrais divulgadas em tweets, o que possibilitou a identificação dos temas mais abordados relacionados à política pública de acesso ao ensino superior do MEC, com destaque para a discussão sobre a Lei de Cotas no Sisu. A classificação das palavras mais destacadas oferece informações relevantes sobre a percepção dos usuários em relação ao Sisu e evidencia aspectos da construção da opinião pública como expressas nas redes sociais sobre as formas de acesso ao ensino superior no Brasil.
Assentos de casamentos da Freguesia de Santo Antônio do Urubu de baixo do Rio São Francisco (1719-1753): ler e escrever conforme as testemunhas
Authors: Assis Lécio Barbosa de , Alves da Silva Jorge Augusto , Pacheco Vera
Published: August 2024

O principal interesse desse estudo é analisar as práticas sociais da cultura escrita, com especial atenção ao exame das assinaturas das testemunhas de casamentos, presentes no primeiro livro de registros paroquiais da Freguesia de Santo Antônio do Urubu de baixo do Rio São Francisco, Capitania de Sergipe d’El Rey do século XVIII. Como base teórico-metodológica, utilizou-se a perspectiva da História Social da Cultura Escrita (CASTILLO GÓMEZ, 1999; 2003; CASTLLO GÓMEZ; SÁEZ, 1994; PETRUCCI, 2000; 2002) e as interfaces necessárias entre a Filologia e a Paleografia (SPINA, 1977; CAMBRAIA, 2005; BERWANGER; LEAL, 2008). Assim, a presente investigação configura-se como um estudo de um corpus diacrônico a partir da leitura e da transcrição paleográfica, descrição e análise das assinaturas das testemunhas de casamentos, produzidas por uma classe dominante e por pessoas socialmente autorizadas para ordenar relações e práticas sociais (CASTILLO GÓMEZ, 2003), refletindo etapas pretéritas das habilidades de ler e escrever, permitindo a realização de um estudo, segundo a caracterização de Magalhães (1996). Os registros de casamentos seguiam a um formulário preestabelecido pelas Ordenações do Sagrado Concílio Tridentino (1545-1563) e das Constituições Primeiras do Arcebispado da Bahia (1707), exarados pelos párocos, que no ato do registro assinavam o documento, juntamente com as testemunhas. Nesse sentido, as questões que se propõe são: quem soube escrever naquele momento particular e quais as relações sociais são representadas pela materialidade da escrita naquele microcosmo social do sertão de baixo do século XVIII? Para essas perguntas, a hipótese inicial é a de que a instrução estava diretamente relacionada com as classes da sociedade e específica para cada sexo, e teria sido este o motivo, o qual determinadas testemunhas não grafaram seus nomes no documento.
redes da literatura: oficina de letramento literário como estratégia de ensino na educação básica e o gênero zine como possibilidade formativa e autoral
Authors: Da Rosa Maria
Published: August 2024

O grupo de pesquisa “Nas redes da literatura”, formado em 2020 e aprovado com apoio financeiro pela agência de fomento local, FAPDF, objetiva realizar oficinas de letramento literário e digital para alunos do ensino médio, com a participação de discentes dos cursos de Letras e Pedagogia como mediadores. O projeto se divide em três etapas: reflexão teórica sobre letramento literário e digital, e noção de autoria; a elaboração das oficinas e materiais didáticos e, por último, a aplicação nas turmas de ensino médio de nossa instituição e interessadas. A metodologia compreende a pesquisa-ação, pois nosso interesse reside em realizar as oficinas pedagógicas com vistas à emancipação dos discentes envolvidos. Seguem a apresentação de algumas atividades, no intuito de publicizar nosso trabalho, promover diálogo com outros grupos e projetos de pesquisa relacionados a estratégias pedagógicas voltadas para a leitura e o letramento digital e, por último, a apresentação dos produtos elaborados na oficina de zine.
The Lambi Model: Haiti, Temporality, and a Holistic Methodology
Authors: Desgranges Magda
Published: August 2024

Abstract: With Haiti at its helm, this article reimagines the conch shell as a methodology of resistance and renewal. The Lambi model is presented to interpret temporal pathways and ancestral practices within African Diaspora lives. Time and space serve as axes of intersection, connecting and delineating points of departure surrounding race, space, power, and freedom. A framework is established through the works of three Haitian writers and activists: Jemima Pierre, Michel-Rolph Trouillot, and Edwidge Danticat. Grounded in an Antillean feminist lens, this formulation of Diaspora identity carries the cadence of a fluid and holistic orientation with ontological, epistemological, and pedagogical implications.
Mina’s Joke in Dracula : The Danger of Women’s Laughter
Authors: Linkin Harriet Kramer
Published: August 2024

ABSTRACT: When Mina first meets Van Helsing in Bram Stoker’s Dracula , she plays a trick on him by giving him the shorthand version of her Whitby diary, which she anticipates he will not be able to read. This essay looks at the central positioning of Mina’s practical joke as an opportunity to consider how Stoker represents women’s capacity to be funny through Lucy, Mina, and Mrs. Bilder, the zookeeper’s wife. The three major theories of humor—superiority, relief, and incongruity, along with nineteenth-century discussions of women and comedy—help clarify how sexualizing women’s laughter through vampirism threatens conventional Victorian sensibilities and masculinity.
Collins’s Heart: Childlike Sympathy and Coincidence in late-Victorian Literature and Science Debates
Authors: Farrar Aileen Miyuki
Published: August 2024

ABSTRACT: Wilkie Collins’s Heart and Science: A Story of the Present Time (1882– 1883) channels the controversy that surrounded debates on vivisection and animal rights at the Victorian fin de siècle . Initial reviewers homed in on Collins’s oversimplified arguments against vivisection, which villainized experimental science and scientists; modern critics emphasize the negative associations casting women of science as absurd practitioners and hysterical patients. This analysis explores how Heart and Science encourages sympathetic dialogue between the arts and science; communicates anxiety in depictions of vivisection and women; and draws meaning and hope from narratives driven by music and children. Through metaphors of acoustic science and plots shaped by border-crossing children, the novel stresses listening as a necessary and healing component in discourses of difference.
Calibration-free scheme for frequency response measurement of a Mach–Zehnder modulator with low-frequency detection
Authors: Jiao Mingqi , Li Lei , Jiang Yuxuan , Lei Congbiao , Xie Liang
Published: August 2024

This paper presents a novel, to the best of our knowledge, calibration-free scheme for measuring the frequency response of Mach–Zehnder modulation (MZM) using low-frequency detection. An auxiliary MZM1 modulated by a MHz-level electrical signal f1 is utilized to generate a double-sideband optical signal, which is subsequently directed into the device under test (MZM2). The MZM2 is biased at its minimum point and driven by a frequency-swept microwave signal f
m
. After photoelectric converting, a fixed low-frequency electrical signal f
L
carrying the frequency response information of the MZM2 is generated. By sweeping f
m
while extracting the amplitude of f
L
, the frequency response of the MZM2 free from the response of the photodetector (PD) is thus determined. In the experiment, the frequency response of a commercial MZM is characterized in the frequency range from 0.1 GHz to 20 GHz with a resolution of 50 MHz. The measurement result is consistent with the vector network analyzer swept method. In addition, the new method eliminates errors introduced by the PD and reduces the requirement for a high-bandwidth PD.
Optimizing LCD structures to mitigate carbon emissions based on root-mean-square values
Authors: Yeh Chia Hung , Chen Wei Min
Published: August 2024

Taiwan is among the leading global producers of display panels, with a GDP as high as 8%. In light of the European Union’s ambitious European Green Deal, which aims for a 55% reduction in carbon emissions by 2030 and carbon neutrality by 2050, the advancement of low-carbon emission panel technology is becoming an inevitable trend. Liquid-crystal display (LCD) technology, known for its non-self-emitting light display, is faced with a significant challenge—the utilization of polarizers and color filters results in a staggering 90% loss of luminance. Therefore, the need to maintain or enhance brightness is crucial for mitigating the carbon footprint. The transition from conventional light-emitting diodes (LEDs) to mini-LEDs has significantly reduced carbon emissions. However, the heat generated by tens of thousands of mini-LEDs poses a new challenge, increasing carbon emissions and raising concerns regarding environmental sustainability. This study focuses on improving the LCD structure to reduce carbon emissions using root-mean-square (RMS) values, with a 32 in. LCD as an example. Through simulations using ANSYS SPEOS optical software, we analyzed the optimal alignment of the mini-LED pitch and the optimal combination of the height and angle of the brightness enhancement film to achieve an RMS value close to 1, which is the target. The most successful outcomes of this analysis include reducing the number of mini-LEDs by 224 pieces, resulting in a 51.02% reduction in carbon emissions while maintaining panel uniformity. This achievement highlights our commitment to environmental protection and sustainable development.
Ground-based simulation of laser link acquisition for inter-satellite laser interferometry
Authors: Hu Qi-Lin , Zhang Jing-Yi , Nie Rui-Liang , Yang Ming-Lin , Cao Bin , Jiao Xi-Xi , Duan Hui-Zong , Ming Min , Huang Xiang-Qing , Zhu Fan , Xu Jie , Yeh Hsien-Chi
Published: August 2024

Laser link acquisition and pointing technique is one of the essential techniques for the inter-satellite laser interferometry for space-based gravitational waves detection and next-generation Earth gravity measurement missions. The first step of building up inter-satellite laser link is using an acquisition camera to capture the inter-satellite laser beam signals within a pre-scanning uncertain cone. Subsequently, high-precision angle measurement technology, namely differential wavefront sensing, is used to achieve a high pointing precision required. Due to the distance constraint of a ground-based simulation experiment, it is difficult to verify directly the feasibility of an inter-satellite laser link acquisition and pointing control scheme. By means of controlling the optical properties of the received laser beam, the long-distance beam propagation is simulated with two optical benches of an inter-satellite interferometer, and the process of a laser link acquisition experiment has been demonstrated. The experimental results show that the inter-satellite laser beams could establish the dual-way locking successfully. The fluctuation of the laser beam pointing direction (in-loop) can be suppressed to about 5 µrad in atmospheric environment. The results verify the feasibility of the laser link acquisition scheme. The experimental setup can be extended to conduct experiments with various parameters, providing technical support for further testing of the inter-satellite laser link acquisition and pointing control methods.
Highly circularly polarized monochromatic high harmonic pulses via a reflective phase retarder at 27.9 eV
Authors: Aksay Furkan , Takahashi Yuta , Sakata Keisuke , Sekikawa Taro
Published: August 2024

A circularly polarized (CP) single-order high harmonic pulse light source, operating at a photon energy of 27.9 eV, is developed. The production of CP harmonic pulses with a degree of polarization exceeding 99% is achieved by utilizing a high-throughput phase retarder composed of SiC mirrors. Notably, our phase retarder exhibits minimal deviation from quarter-wave phase retardation, with a precision of less than ±λ/50 across a 3.1 eV bandwidth. This wide bandwidth enables effective polarization conversion of attosecond pulses preserved. By implementing the phase retarder, we converted the linear polarization to circular with an ellipticity of 0.93.
X-ray image reconstruction for continuous acquisitions with a generalized motion model
Authors: Huyge Ben , Renders Jens , Sanctorum Joaquim G. , De Beenhouwer Jan , Sijbers Jan
Published: August 2024

Continuous X-ray imaging is known to reduce mechanical vibrations and scan time compared to a step-and-shoot acquisition approach. However, motion during X-ray exposure leads to blurred projections and consequently to loss of spatial resolution and contrast in conventionally reconstructed images. Recent works that aim to reduce continuous motion blur focus only on rotational motion and often include linearization approximations, while many applications would benefit from a more generalized continuous acquisition strategy. In this paper, we propose a dedicated reconstruction technique for rotational, translational, and roto-translational motion, without requiring a linearization approximation. Through simulations and real experiments, we show that motion blur artifacts caused by roto-translational continuous scanning are substantially reduced, allowing for faster scanning while retaining image quality.
Theoretical probability distribution model and reduction techniques based on an interleaved DFT spread for PAPR in a digital sub-carrier multiplexing system
Authors: Xie Fei , Tang Du , Huang Xiaoqian , Liu Shuangyue , Yang Aiying , Qiao Yaojun
Published: August 2024

This paper presents a theoretical probability distribution model for peak-to-average power ratio (PAPR) in the digital sub-carrier multiplexing (DSCM) system, which has not previously been proposed in the literature. To reduce PAPR, an interleaved discrete Fourier transform spread DSCM (I-DFT-S-DSCM) scheme is proposed, which introduces reversible correlations between subcarriers. To investigate the effectiveness of the proposed schemes, a 64-GBaud 16 quadrature amplitude modulation (16-QAM) DSCM system with 4, 8, and 16 sub-carriers was constructed. In the digital domain, the results demonstrate that the proposed theoretical PAPR probability distribution model exhibits mean squared errors (MSE) below 10−5 for the observed and model-predicted complementary cumulative distribution functions (CCDF) in both DSCM and I-DFT-S-DSCM schemes. Regarding PAPR reduction, the I-DFT-S-DSCM scheme demonstrated a reduction in PAPR of up to 1.44 dB compared to the conventional DSCM scheme. To further investigate the impact of PAPR on the bit error rate (BER) performance of the DSCM system, the I-DFT-S-DSCM scheme is implemented with 8 subcarriers transmitted over a 100-km standard single-mode fiber (SSMF). A comparative analysis with DSCM indicates that I-DFT-S-DSCM achieves a PAPR reduction of approximately 1.1 dB and improves receiver sensitivity by approximately 0.7 dB at a 7% hard-decision forward error correction (HD-FEC) threshold, in 100-km single-mode fiber SSMF transmissions.
Optical continuous pulse position modulation-based analog RoF via frequency-domain position estimation
Authors: Xu Yicheng , Zhu Yixiao , Fu Mengfan , Hu Weisheng , Zhuge Qunbi
Published: August 2024

Analog radio-over-fiber (A-RoF) solutions for mobile fronthaul are regaining wide attention due to their high spectral efficiency and low complexity. However, the performance of A-RoF is usually limited by the fiber link fidelity. In this Letter, we propose and experimentally demonstrate an optical continuous pulse position modulation-based analog radio-over-fiber (OCPPM-RoF) scheme, in which the amplitudes of wireless waveforms are mapped to the time-domain positions of optical pulses to decouple the additive noise. The de-modulation of OCPPM-RoF signals is performed by a frequency-domain continuous position estimation (FD-CPE) algorithm including cross-power spectrum calculation and weighted least square for accurate delay estimation. In the experiment, by adopting appropriate pulse width factors, the recovered signal-to-noise ratio (SNR) can be flexibly adjusted within a wide range from 31.8 to 54.0 dB, supporting the transmission of various formats from 256-QAM to 65536-QAM. The results indicate that OCPPM-RoF can be a promising candidate for future fronthaul.
Ti3CN Mxene-microfiber integrated waveguide for high stability four-wave mixing effect generation
Authors: Sui Lu , Zhao Qianfu , Sun Chang , Wang Tianshu , Lu Ming
Published: August 2024

The application of two-dimensional (2D) materials in third-order nonlinear optics and integrated waveguide technologies is further explored. Specifically, we synthesized Ti3CN MXene via acid etching and subsequently coated it onto highly nonlinear microfibers (HNLMF) using optical deposition techniques. This approach enabled the development of integrated waveguides that exhibit a robust nonlinear response. Our comprehensive analysis highlights the key attributes of Ti3CN, including its band structure and enhanced nonlinear optical properties, which contribute to significant improvements in all-optical wavelength conversion (AOWC). At an operational wavelength of 2.05 µm, the Ti3CN-HNLMF integrated waveguide through the four-wave mixing (FWM) effect demonstrated a conversion efficiency of -29.54 dB, with a wavelength separation of 14 nm and a minimal fluctuation in conversion efficiency (0.43 dB) sustained over 520 minutes. The findings from this study not only demonstrate a practical method for improving AOWC but also offer insights into the potential of MXenes in integrated waveguide technologies, thereby supporting the development of advanced nonlinear optical devices.
Ultrastable vacuum-gap Fabry–Perot cavities operated in air
Authors: Liu Yifan , Jin Naijun , Lee Dahyeon , McLemore Charles , Nakamura Takuma , Kelleher Megan , Cheng Haotian , Schima Susan , Hoghooghi Nazanin , Diddams Scott , Rakich Peter , Quinlan Franklyn
Published: August 2024

We demonstrate a vacuum-gap ultrastable optical reference cavity that
does not require a vacuum enclosure. Our simple method of optical
contact bonding in a vacuum environment allows for cavity operation in
air while maintaining vacuum between the cavity mirrors. Vacuum is
maintained long term, with no observed degradation in cavity stability
for over 1 year after bonding. For a 1550 nm laser
stabilized to a 9.7 mL in-vacuum bonded cavity, the measured
Allan deviation is 2.4×10−14 at 1 s, and its phase noise is
thermal-noise-limited from 0.1 Hz to 10 kHz, reaching
about −105dBc/Hz at 10 kHz offset frequency.
This represents the highest stability of any oscillator operated
without a vacuum enclosure, to our knowledge. Furthermore, we
demonstrate a 0.5 mL in-vacuum bonded cavity created using
microfabricated mirrors and cavity dicing, with phase noise reaching −95 dBc/Hz at 10 kHz offset frequency. By
relieving the need for high-vacuum enclosures, we greatly enhance the
portability and utility of low-noise, compact, cavity-stabilized
lasers, with applications ranging from environmental sensing to mobile
optical clocks to ultralow-noise microwave generation.
Introduction of Modified Anomalous Vortex Beam with Self-Focusing Properties
Authors: Mingjian Cheng , Al-Ahsab Hassan , Cao Yuancong , Zhang Huan , Yi Xiang , Xu YAN , Guo Lixin
Published: August 2024

This study introduces and experimentally demonstrates the concept of a Modified Anomalous Vortex Beam (MAVB), which carries Orbital Angular Momentum (OAM) and exhibits unique self-focusing properties. Utilizing holographic techniques and customized phase masks, we precisely control the beam’s phase and intensity distribution, enhancing self-focusing behavior while preserving traditional anomalous vortex beam features. We derive an analytical formula to describe MAVB propagation within a paraxial ABCD optical system. The self-focusing characteristics are influenced by initial parameters such as beam order, quantum number, beam waist, wavelength, and the modification parameter. Additionally, we simulate MAVB propagation and their OAM spectrum in maritime atmospheric turbulence. Through comprehensive theoretical analysis and experimental validation, we show how MAVBs achieve controlled self-focusing, leading to enhanced beam control and stability. Our study explores the mechanisms, design principles, and practical implications of MAVBs, emphasizing their potential to revolutionize optical applications
IT – Enabler der Energiewende
Authors: Hooß Kerstin , Knoll Matthias , Welter Jürgen
Published: August 2024

Der Umbau des Energiesystems von einer weitgehend hierarchischen hin zu einer stark dezentralisierten und nachhaltigen Struktur erfordert umfassende Überlegungen zur Entwicklung geeigneter IT-Lösungen. Dabei beeinflussen einerseits der Stand technischer Entwicklungen, andererseits der Stand der Regulatorik und Standardisierung die Verfügbarkeit und die Akzeptanz „passender“ Anwendungssysteme. Es wird zudem deutlich, dass weniger das Fehlen innovativer Ansätze in der IT, als vielmehr geeignete Wege zur „richtigen“ Kombination bereits verfügbarer – und vielfach auch bereits in anderen Bereichen bewährter – Technologien und Komponenten den notwendigen niederschwelligen IT-Einsatz erschweren. Dieser Einführungsbeitrag stellt daher ausgehend von den Besonderheiten des im Umbau befindlichen Energiesystems zentrale Technologien, Konzepte und Elemente im IT-Kontext vor, die notwendig sind, um die Herausforderungen bewältigen zu können. Ein Ausblick rundet den Beitrag ab.
DepoScope: Accurate phage depolymerase annotation and domain delineation using large language models
Authors: Concha-Eloko Robby , Stock Michiel , De Baets Bernard , Briers Yves , Sanjuán Rafael , Domingo-Calap Pilar , Boeckaerts Dimitri
Published: August 2024

Bacteriophages (phages) are viruses that infect bacteria. Many of them produce specific enzymes called depolymerases to break down external polysaccharide structures. Accurate annotation and domain identification of these depolymerases are challenging due to their inherent sequence diversity. Hence, we present DepoScope, a machine learning tool that combines a fine-tuned ESM-2 model with a convolutional neural network to identify depolymerase sequences and their enzymatic domains precisely. To accomplish this, we curated a dataset from the INPHARED phage genome database, created a polysaccharide-degrading domain database, and applied sequential filters to construct a high-quality dataset, which is subsequently used to train DepoScope. Our work is the first approach that combines sequence-level predictions with amino-acid-level predictions for accurate depolymerase detection and functional domain identification. In that way, we believe that DepoScope can greatly enhance our understanding of phage-host interactions at the level of depolymerases.
Quantitative drug susceptibility testing for Mycobacterium tuberculosis using unassembled sequencing data and machine learning
Authors:   The CRyPTIC consortium
Published: August 2024

There remains a clinical need for better approaches to rapid drug susceptibility testing in view of the increasing burden of multidrug resistant tuberculosis. Binary susceptibility phenotypes only capture changes in minimum inhibitory concentration when these cross the critical concentration, even though other changes may be clinically relevant. We developed a machine learning system to predict minimum inhibitory concentration from unassembled whole-genome sequencing data for 13 anti-tuberculosis drugs. We trained, validated and tested the system on 10,859 isolates from the CRyPTIC dataset. Essential agreement rates (predicted MIC within one doubling dilution of observed MIC) were above 92% for first-line drugs, 91% for fluoroquinolones and aminoglycosides, and 90% for new and repurposed drugs, albeit with a significant drop in performance for the very few phenotypically resistant isolates in the latter group. To further validate the model in the absence of external MIC datasets, we predicted MIC and converted values to binary for an external set of 15,239 isolates with binary phenotypes, and compare their performance against a previously validated mutation catalogue, the expected performance of existing molecular assays, and World Health Organization Target Product Profiles. The sensitivity of the model on the external dataset was greater than 90% for all drugs except ethionamide, clofazimine and linezolid. Specificity was greater than 95% for all drugs except ethambutol, ethionamide, bedaquiline, delamanid and clofazimine. The proposed system can provide quantitative susceptibility phenotyping to help guide antimicrobial therapy, although further data collection and validation are required before machine learning can be used clinically for all drugs.
A quantitative description of light-limited cyanobacterial growth using flux balance analysis
Authors: Höper Rune , Komkova Daria , Zavřel Tomáš , Steuer Ralf
Published: August 2024

The metabolism of phototrophic cyanobacteria is an integral part of global biogeochemical cycles, and the capability of cyanobacteria to assimilate atmospheric CO2 into organic carbon has manifold potential applications for a sustainable biotechnology. To elucidate the properties of cyanobacterial metabolism and growth, computational reconstructions of genome-scale metabolic networks play an increasingly important role. Here, we present an updated reconstruction of the metabolic network of the cyanobacterium Synechocystis sp. PCC 6803 and its quantitative evaluation using flux balance analysis (FBA). To overcome limitations of conventional FBA, and to allow for the integration of experimental analyses, we develop a novel approach to describe light absorption and light utilization within the framework of FBA. Our approach incorporates photoinhibition and a variable quantum yield into the constraint-based description of light-limited phototrophic growth. We show that the resulting model is capable of predicting quantitative properties of cyanobacterial growth, including photosynthetic oxygen evolution and the ATP/NADPH ratio required for growth and cellular maintenance. Our approach retains the computational and conceptual simplicity of FBA and is readily applicable to other phototrophic microorganisms.
Reliable estimation of tree branch lengths using deep neural networks
Authors: Suvorov Anton , Schrider Daniel R.
Published: August 2024

A phylogenetic tree represents hypothesized evolutionary history for a set of taxa. Besides the branching patterns (i.e., tree topology), phylogenies contain information about the evolutionary distances (i.e. branch lengths) between all taxa in the tree, which include extant taxa (external nodes) and their last common ancestors (internal nodes). During phylogenetic tree inference, the branch lengths are typically co-estimated along with other phylogenetic parameters during tree topology space exploration. There are well-known regions of the branch length parameter space where accurate estimation of phylogenetic trees is especially difficult. Several novel studies have recently demonstrated that machine learning approaches have the potential to help solve phylogenetic problems with greater accuracy and computational efficiency. In this study, as a proof of concept, we sought to explore the possibility of machine learning models to predict branch lengths. To that end, we designed several deep learning frameworks to estimate branch lengths on fixed tree topologies from multiple sequence alignments or its representations. Our results show that deep learning methods can exhibit superior performance in some difficult regions of branch length parameter space. For example, in contrast to maximum likelihood inference, which is typically used for estimating branch lengths, deep learning methods are more efficient and accurate. In general, we find that our neural networks achieve similar accuracy to a Bayesian approach and are the best-performing methods when inferring long branches that are associated with distantly related taxa. Together, our findings represent a next step toward accurate, fast, and reliable phylogenetic inference with machine learning approaches.
Practice of district health information data for decision making and associated factors among performance monitoring team at Hadiya Zone Public Health Facilities SNNPR, Ethiopia
Authors: Madebo Merkineh Mekebo , Elitro Yoseph Olonjo , Sundako Bereket Birege , Anore Adimasu Jemal , Ashegire Muluken , Funga Mengistu Lodebo , Lalore Marta Tesema , Samuel Abriham
Published: August 2024

Background

Evidence based practice is a key tool to increase effectiveness and efficiency of healthcare providers worldwide and using health facility data at all levels is vital. But, it is poorly practiced in developing countries including Ethiopia. As a result, the purpose of this study was to evaluate the level of practice of District Health Information for decision making and associated factors among performance monitoring teams in Hadiya Zone public health facilities, South Nation Nationality People Republic, Ethiopia, in 2022

Methods

A facility based-cross sectional study was employed from May 3 to June 3, 2022. To obtain data, a pre-tested structured questionnaire with qualitative was employed. A multistage random sampling technique was employed to select performance monitoring team from public health facilities. Data was entered into a computer using Epi data version 4.6, and analyzed using SPSS version 25. Bivariable and multivariable analyses were used to identify determinants related to practice of district health information. For the qualitative section, thematic analysis was used.

Results

The practice of district health information for decision making among performance monitoring team in this study was 48% (95% CI: [42.3, 54.1]). having standard sets of indicators [AOR = 4.055; 95% CI: (1.67, 9.86)], Being trained [AOR = 3.12; 95%CI: (1.385, 7.023)], having internet access [AOR = 3.23; 95% CI: (1.52, 6.9)], having positive attitudes [AOR = 2.667; 95% CI: (1.28, 5.56)], having low motivation [AOR = 0.202; 95% CI: (0.081, 0.504)], Sufficient skill [AOR = 3.239: 95%CI; (1.328, 8.164)] and having knowledge [AOR = 6.227; 95% CI: (2.12, 12.8)] were significantly associated with practice of District health information for decision making.

Conclusion

In general, this study found that the performance monitoring team at health facilities poorly practiced district health information. It requires major improvement to provide a consistent set of indicators, training, internet access, user attitudes, motivation, and necessary skills and knowledge, as well as to raise users’ confidence in DHIS2.
Creating a data collection and management platform to support measurement of adolescent HIV care transition processes within low- and middle-income countries: The GRADUATE project
Authors: Tsondai Priscilla R. , Davies Mary-Ann , Singtoroj Thida , Maxwell Nicola , Technau Karl-Günter , Chokephaibulkit Kulkanya , Lumbiganon Pagakrong , Sohn Annette H. ,   on behalf of the Global fRAmework of Data collection Used for Adolescent HIV Transition Evaluation (GRADUATE) Advisory Group
Published: August 2024

Few national programs and research cohorts within low- and middle-income countries (LMICs) document transition-related processes and outcomes for adolescents and young adults living with HIV (AYLH) transitioning to adulthood. Between 2017–2020, The Global fRAmework of Data collection Used for Adolescent HIV Transition Evaluation (GRADUATE) project convened a collaborative advisory group to identify key variables and definitions capturing the process, predictors, and outcomes across the transition period. In total, 114 variables identified as essential to measuring AYLH transition-related data were identified and formatted into a GRADUATE Data Exchange Standard (DES), which was added to and harmonized with the existing International epidemiology Databases to Evaluate AIDS (IeDEA) DES. In 2019, the GRADUATE DES was pilot tested at four IeDEA facilities in Malawi, South Africa, and Thailand through a cross-sectional study. Upon comparing the variables to routine medical records, available data were too limited to adequately capture transition-related processes and outcomes. However, additional data collection using GRADUATE tools was feasible and improved completeness. Of the 100 (52% female) AYLH included in the pilot study, 71% had transitioned/transferred to adult care, with 42% transitioning from an adolescent-specific model of care within an integrated family clinic to having their clinic visits scheduled on a different day of the week while 58% transferred from a pediatric facility to one offering adult HIV care. While almost all (94%) had a transition-related discussion with their healthcare providers prior to the transition, we found that 69% (95% CI 49–85%) were somewhat or very satisfied/comfortable with the post-transfer clinic and the staff. Utilization of the GRADUATE DES better characterized AYLH transitioning to adulthood across LMICs, and optimally measured transition preparation activities and outcomes. Utilization of the GRADUATE DES in other settings could facilitate comparisons and identify gaps in the care of transitioning adolescents that need to be addressed.
The risk and risk factors of chikungunya virus infection and rheumatological sequelae in a cohort of U.S. Military Health System beneficiaries: Implications for the vaccine era
Authors: Pollett Simon , Hsieh Hsing-Chuan , Lu Dan , Grance Melissa , Richard Stephanie , Nowak Gosia , Lanteri Charlotte , Tribble David , Burgess Timothy
Published: August 2024

Background

Understanding the risk of chikungunya virus (CHIKV) infection and rheumatic sequelae across populations, including travelers and the military, is critical. We leveraged healthcare delivery data of over 9 million U.S. Military Health System (MHS) beneficiaries to identify cases, and sampled controls, to estimate the risk of post-CHIKV rheumatic sequelae.

Methodology/principal findings

MHS beneficiary CHIKV infections diagnosed 2014–2018 were identified from the Disease Reporting System internet, TRICARE Encounter Data Non-Institutional, and Comprehensive Ambulatory/Professional Encounter Record systems. Non-CHIKV controls were matched (1:4) by age, gender, beneficiary status, and encounter date. The frequency of comorbidities and incident rheumatic diagnoses through December 2018 were derived from International Classification of Diseases codes and compared between cases and controls. Poisson regression models estimated the association of CHIKV infection with rheumatic sequelae. We further performed a nested case-control study to estimate risk factors for post-CHIKV sequelae in those with prior CHIKV. 195 CHIKV cases were diagnosed between July 2014 and December 2018. The median age was 42 years, and 43.6% were active duty. 63/195 (32.3%) of CHIKV cases had an incident rheumatic diagnosis, including arthralgia, polyarthritis, polymyalgia rheumatica, and/or rheumatoid arthritis, compared to 156/780 (20.0%) of controls (p < 0.001). CHIKV infection remained associated with rheumatic sequelae (aRR = 1.579, p = 0.008) after adjusting for prior rheumatic disease and demography. Those with rheumatic CHIKV sequelae had a median 7 healthcare encounters (IQR 3–15). Among CHIKV infections, we found no association between post-CHIKV rheumatic sequelae and demography, service characteristics, or comorbidities.

Conclusions/significance

CHIKV infection is uncommon but associated with rheumatic sequelae among MHS beneficiaries, with substantial healthcare requirements in a proportion of cases with such sequelae. No demographic, clinical, or occupational variables were associated with post-CHIKV rheumatic sequelae, suggesting that prediction of these complications is challenging in MHS beneficiaries. These findings are important context for future CHIKV vaccine decision making in this and other populations.
Acute Q fever in patients with an influenza-like illness in regional New South Wales, Australia
Authors: Rodrigo Chaturaka , Walker Gregory , Sevendal Andrea T. K. , Nguyen Chelsea , Stelzer-Braid Sacha , Rawlinson William , Graves Stephen , Gidding Heather F. , Stenos John , Lloyd Andrew R.
Published: August 2024

Introduction

Query (Q) fever is a zoonosis caused by the bacterium Coxiella burnetii typically presenting as an influenza-like illness (ILI) with or without hepatitis. The infection may be missed by clinicians in settings of low endemicity, as the presentation is clinically not specific, and there are many more common differential diagnoses for ILI including SARS-CoV-2 infection.

Methods

Residual serum samples were retrospectively tested for Phase 1 and 2 Q fever-specific IgM, IgG, IgA antibodies by indirect immunofluorescence and C. burnetii DNA by polymerase chain reaction. They had not been previously tested for Q fever, originating from undiagnosed patients with probable ILI, aged 10–70 years and living in regional New South Wales, Australia. The results were compared with contemperaneous data on acute Q fever diagnostic tests which had been performed based on clinicians requests from a geographically similar population.

Results

Only one (0.2%) instance of missed acute Q fever was identified after testing samples from 542 eligible patients who had probable ILI between 2016–2023. Laboratory data showed that during the same period, 731 samples were tested for acute Q fever for clinician-initiated requests and of those 70 (9.6%) were positive. Probability of being diagnosed with Q fever after a clinician initiated request was similar regardless of the patients sex, age and the calendar year of sampling.

Conclusion

In this sample, Q fever was most likely to be diagnosed via clinician requested testing rather than by testing of undiagnosed patients with an influenza like illness.
Lumpy skin disease diagnosis in cattle: A deep learning approach optimized with RMSProp and MobileNetV2
Authors: Muhammad Saqib Sheikh , Iqbal Muhammad , Tahar Ben Othman Mohamed , Shahazad Tariq , Yasin Ghadi Yazeed , Al-Amro Sulaiman , Mazhar Tehseen
Published: August 2024

Lumpy skin disease (LSD) is a critical problem for cattle populations, affecting both individual cows and the entire herd. Given cattle’s critical role in meeting human needs, effective management of this disease is essential to prevent significant losses. The study proposes a deep learning approach using the MobileNetV2 model and the RMSprop optimizer to address this challenge. Tests on a dataset of healthy and lumpy cattle images show an impressive accuracy of 95%, outperforming existing benchmarks by 4–10%. These results underline the potential of the proposed methodology to revolutionize the diagnosis and management of skin diseases in cattle farming. Researchers and graduate students are the audience for our paper.
Biofilm formation, agr typing and antibiotic resistance pattern in methicillin-resistant Staphylococcus aureus isolated from hospital environments
Authors: Rimi Sabrina Sultana , Ashraf Md. Nahid , Sigma Sanzila Hossain , Ahammed Md. Tanjir , Siddique Mahbubul Pratik , Zinnah Mohammad Ali , Rahman Md. Tanvir , Islam Md. Shafiqul
Published: August 2024

Biofilm development significantly enhances the virulence of methicillin-resistant Staphylococcus aureus (MRSA), leading to severe infections and decreased susceptibility to antibiotics, especially in strains associated with hospital environments. This study examined the occurrence of MRSA, their ability to form biofilms, agr typing, and the antibiotic resistance profiles of biofilm-forming MRSA strains isolated from environmental surfaces at Mymensingh Medical College Hospital (MMCH). From 120 swab samples, 86 (71.67%) tested positive for S. aureus. MRSA was identified in 86 isolates using the disk diffusion technique, and by polymerase chain reaction (PCR), 56 (65.1%) isolates were confirmed to carry the mecA gene. The Crystal Violet Microtiter Plate (CVMP) test revealed that 80.35% (45 isolates) were biofilm-forming and 19.6% (11 isolates) were non-biofilm-forming. Out of 45 biofilm producer isolates 37.5% and 42.9% isolates exhibited strong and intermediate biofilm-forming characteristics, respectively. Molecular analysis revealed that 17.78% of MRSA isolates carried at least one gene related to biofilm formation, specifically icaA, icaB, and icaD genes were discovered in 13.33%, 8.89%, 6.67% of the MRSA isolates, respectively. In agr typing, the most prevalent group was agr I (71.11%), followed by group III (17.78%) and group II (11.11%). Group IV was not detected. The distribution of agr gene groups showed a significant difference among biofilm-forming isolates (p < 0.05). In agr group I, 18.75% of isolates carried the icaA gene, 12.5% carried the icaB gene, and 9.37% carried the icaD gene. Biofilm-forming genes were not detected in any of the isolates from agr groups II or III. There are no statistically significant differences between agr groups and the presence of these genes (p > 0.05). Antibiotic resistance varied significantly among agr groups, with agr group I displaying the highest resistance, agr group II, and agr group III exhibiting the least resistance (p < 0.05). Seventy-three (73.3%) of the isolates were multi-drug resistant, with agr group I displaying nineteen MDR patterns. The occurrence of MRSA in hospital environments and their capacity to form biofilm raises concerns for public health. These findings support the importance of further research focused on agr quorum sensing systems as a basis for developing novel antibacterial agents.