bluuebunny/crossref_metadata_2025 huggingface dataset:
A systematic review on application of next-generation sequencing on microbes isolated from cultured species
Authors: Sing Yee Yap , Mohamad Tahir Nur Diyana , Mohamed Din Mohamed Shariff , Uda Zahli Nurul Izzati
Published: November 2023

Background This study employs NGS for analyzing microbes in cultured species. It follows PRISMA guidelines to systematically investigate NGS’s role in identifying pathogens from cultured species. Methods Following PRISMA guidelines, Scopus and ScienceDirect were systematically searched for studies on next-generation sequencing (NGS) from 2012 to 2023. Articles lacking relevant data or keywords were excluded. Quality limitations were acknowledged. To reduce bias, ROBINS-I tool was used to assess bias across seven domains. Data were organized in a matrix table, facilitating detailed analysis and visualization. This systematic approach ensured a transparent, comprehensive review of NGS in microbiology. Results 956 and 200 articles were available and reviewed from Scopus and ScienceDirect, respectively, using keywords such as next generation sequencing, cultured species and microbes. Only 6 articles are related to this topic and within 10 years of publication to ensure up to date information. Three of them are reported from China, one from Mexico, one from Australia and one from United States of America. Most of the articles reported they are using Illumina platform more than Nanopore platform. 4 out of 6 articles of them are using Illumina while 2 out of 6 articles are using nanopore platform. The microbes identified using those next generation sequencing are microsporidia Enterocytozoan hepatopenaei (EHP), fathead minnow calicivirus (FHMCV), mud crab reovirus (MCRV), white spot syndrome virus (WSSV), and fungal species such as Pneumocystis jirovecii. Conclusions In conclusion, Illumina sequencing is more commonly employed platform for identifying pathogens in cultured species compared to Nanopore sequencing. China stands out as the leading contributor to NGS research in this context. However, it’s important to acknowledge potential limitations in the study due to the quality of the articles reviewed and the risk of bias assessment.
Protocol for a cluster randomised controlled trial to evaluate effectiveness of a self-help group intervention to encourage smoke-free homes in slums of Kochi(Kochi Intervention for tobacco smoke free homes-KIFT)
Authors: Sreedevi Aswathy , Krishnapillai Vijayakumar , Thulaseedharan Jissa Vinoda , Irazola Vilma , Krishnan Sajitha , Kunoor Akhilesh , Menon Jaideep Chanavil , Danaei Goodarz
Published: November 2023

Background Exposure to second hand smoke (SHS) is a cause for heart disease and lung cancer among non- smokers. This cluster randomized control trial will evaluate the effectiveness of a tobacco smoke free home intervention in reducing exposure to second hand smoke. Protocol The intervention will be conducted among 30 clusters in urban and peri-urban areas of Kochi, India. The sample size is 300 per arm and 15 clusters to detect a minimal difference of 0.03ng/ml in cotinine levels between groups, at 80% power with a two-sided alfa of 0.05 considering variable cluster size. A baseline survey will be undertaken to identify smokers. Data related to smoking, indoor smoking, nicotine dependence, blood pressure (BP) of smokers, morbidity experienced, and lung volume Fev1/Fev6 of smokers will be measured. Urine cotinine, morbidity, BP of spouse and child will be assessed. Air quality monitors measuring PM2.5 will be placed in homes. Trained self-help group women and frontline health workers will implement the intervention. The intervention will consist of monthly home visits to educate the smoker on the harms of second-hand smoke using 3 A’s. The circle of influencers around the smoking men will also be contacted by the members of self-help group to provide support to stop smoking within homes and to quit. They will then organize two-three meetings of community leaders and heads of women’s groups, present data on harms of SHS, and explain the rationale for establishing smoke free homes in their community for a duration of six months. After the intervention a post assessment will be conducted and this will be repeated after six months. Ethics and dissemination The trial protocol was approved by the Institutional Ethical Committee of Amrita Institute of Medical Sciences. Results will be submitted to open access peer reviewed journals and shared with other stakeholders. Trial registration CTRI/2021/06/034478
Case Report: Cryoglobulinemic vasculitis after COVID-19 vaccination
Authors: Kechaou Ines , Tekaya Asma , Hamdi Mohamed Salah , Jebri Meryem , Cherif Eya , Ben Hassine Lamia
Published: November 2023

Since its occurrence, the coronavirus disease 2019 (COVID-19) pandemic has been responsible for a substantial rate of morbidity and mortality. The quick development of an effective and safe vaccine was essential in order to control the ongoing pandemic. However, given the severity of the situation, mass-scale vaccination had to be undertaken without much hindsight. Subsequently, side effects of the anti-COVID-19 vaccine, such as autoimmune diseases, have been reported. Cryoglobulinemic vasculitis (CryoVas) is a rare auto-immune disease, caused by the presence in the serum of abnormal immunoglobulins (cryoglobulins) able to precipitate at temperatures below 37°C. CryoVas can be either essential or, more frequently, secondary to other diseases such as infections, malignancies and auto-immune diseases. In some cases, CryoVas can be vaccine-induced. We describe an original case of a 57-year-old woman with no medical history who presented with purpura of the lower limbs that appeared 5 days after receiving her first COVID-19 vaccine. Skin biopsy and immunological work out were consistent with CryoVas.
A multi-spectral myelin annotation tool for machine learning based myelin quantification
Authors: Çapar Abdulkerim , Çimen Sibel , Aladağ Zeynep , Ekinci Dursun Ali , Ayten Umut Engin , Kerman Bilal Ersen , Töreyin Behçet Uğur
Published: November 2023

Myelin is an essential component of the nervous system and myelin damage causes demyelination diseases. Myelin is a sheet of oligodendrocyte membrane wrapped around the neuronal axon. In the fluorescent images, experts manually identify myelin by co-localization of oligodendrocyte and axonal membranes that fit certain shape and size criteria. Because myelin wriggles along x-y-z axes, machine learning is ideal for its segmentation. However, machine-learning methods, especially convolutional neural networks (CNNs), require a high number of annotated images, which necessitate expert labor. To facilitate myelin annotation, we developed a workflow and software for myelin ground truth extraction from multi-spectral fluorescent images. Additionally, to the best of our knowledge, for the first time, a set of annotated myelin ground truths for machine learning applications were shared with the community.
Impact of the COVID-19 pandemic on routine surveillance for adults with chronic hepatitis B virus (HBV) infection in the UK
Authors: Campbell Cori , Wang Tingyan , Smith David A. , Freeman Oliver , Noble Theresa , Várnai Kinga A , Harris Steve , Salih Hizni , Roadknight Gail , Little Stephanie , Glampson Ben , Mercuri Luca , Papadimitriou Dimitri , Jones Christopher R , Taylor Vince , Chaudhry Afzal , Phan Hang , Borca Florina , Olza Josune , Warricker Frazer , Romão Luis , Ramlakhan David , English Louise , Klenerman Paul , Andersson Monique I. , Collier Jane , Nastouli Eleni , Khakoo Salim I. , Gelson William , Cooke Graham S. , Woods Kerrie , Davies Jim , Barnes Eleanor , Matthews Philippa C.
Published: November 2023

Background To determine the impact of the COVID-19 pandemic on the population with chronic Hepatitis B virus (HBV) infection under hospital follow-up in the UK, we quantified the coverage and frequency of measurements of biomarkers used for routine surveillance (alanine transferase [ALT] and HBV viral load). Methods We used anonymized electronic health record data from the National Institute for Health Research (NIHR) Health Informatics Collaborative (HIC) pipeline representing five UK National Health Service (NHS) Trusts. Results We report significant reductions in surveillance of both biomarkers during the pandemic compared to pre-COVID-19 years, both in terms of the proportion of patients who had ≥1 measurement annually, and the mean number of measurements per patient. Conclusions These results demonstrate the real-time utility of HIC data in monitoring health-care provision, and support interventions to provide catch-up services to minimise the impact of the pandemic. Further investigation is required to determine whether these disruptions will be associated with increased rates of adverse chronic HBV outcomes.
A STUDY OF OPTICAL SURFACE ANALYSIS METHODS FOR 3D PRINTED CONTINUOUS FIBER COMPOSITES
Authors: RAHMAN MD ATIKUR , HOSSAIN ARAFAT BIN , ISLAM MD ZAHIRUL , HALL ERIC , GIBBON LUKE , ULVEN CHAD A. , LASCALA JOHN J.
Published: November 2023

Continuous fiber reinforced additive manufacturing has been growing in research and in commercial application. In this work, additively manufactured carbon fiber thermoset composites are being produced utilizing a liquid deposition modeling process with photo-curable resin. The quality and mechanical properties of additively manufactured composites is sensitive to the void concentration and distribution. The void percentage of additively manufactured composites had shown correlation with the surface quality of individual layers. Research has found that surface quality of individual layers could be controlled by process parameter adjustments such as material flow rate, speed and layer thickness. Regular monitoring of these variables becomes necessary for consistent and feasible production. To achieve this, the authors implemented a study utilizing a camera system and image processing algorithm for surface evaluation with a goal of print parameter adjustment on the fly. The resulting technology has been proven to accurately analyze each layer. This study aims to develop a surface feature extraction method for the purpose of training and deployment of a machine learning algorithm which will execute dynamic adjustment of process parameters.
PREDICTION OF DISTORTION AND RESIDUAL STRESS EVOLUTION IN THE FUSED FILAMENT FABRICATION PROCESS USING HIGHER-ORDER FINITE ELEMENTS
Authors: NAGARAJ MANISH , HANSEN CHRISTOPHER J. , MAIARU MARIANNA
Published: November 2023

This work presents a higher-order finite element-based process modeling framework for material extrusion additive manufacturing. The numerical modeling is based on higher-order structural theories derived via the Carrera Unified Formulation, and allows for high-fidelity modeling in a computationally efficient manner. The element activation strategy is employed to simulate the material deposition process. A thermo-mechanical analysis is performed to determine the evolving temperature field within the part during the printing process, which is subsequently used to evaluate the distortion of the printed structure. Numerical assessments are performed, and the agreement of the numerical predictions with available reference experimental data validates the proposed process modeling framework for additive manufacturing.
MACHINE LEARNING BASED STRUCTURAL AND FAILURE CHARACTERISTICS OF CARBON NANOTUBE JUNCTION CONFIGURATIONS
Authors: UNNIKRISHNAN VINU , VARSHNEY VIKAS , GABER LANDON , CASTLE JAMES , ROY AJIT
Published: November 2023

Carbon nanotube based multi-terminal junction configurations are of great interest because of their potential aerospace and electronics applications. The performance of nanodevices based on these carbon nanotube junctions can be affected by the structural properties of the topologically accurate junction morphology like mechanical strength, thermal and electrical conductivities. It is therefore necessary to be able to investigate and characterize these properties accurately and quickly such that optimum structural configurations can be intelligently configured for the desired function. It is in this scenario that traditional atomistic simulations encounter severe limitations in terms of computational time required and hence the use of artificial intelligence techniques becomes necessary. In this work, we present a Machine Learning based characterization of structural and failure properties of carbon nanotube junction configurations. Structural and failure properties of a large set of 3D nanotube (CNT) junction configurations are first studied using molecular dynamics (MD) simulations. The stress-strain data until failure for each of the carbon nanotube junction configuration was estimated and various structural properties were used in the generation of the dataset. This dataset was used in a gradient boosting-based machine learning algorithm for the characterization of mechanical and failure properties of the nanotube junctions. Gradient boosting algorithms are prediction-based models that consists of sequential ensemble learning techniques in which the overall performance of the model is enhanced over multiple iterations. The coefficient of determination (R2) value is used to evaluate the robustness of the developed models for structural and failure parameters identified earlier. The machine learning techniques can be effective in predicting the structural properties of nanotube junction configurations with greater confidence.
Practice Summary: General Electric Company Optimizes Wind Turbine Towers Sourcing and Logistics Operations
Authors: Bollapragada Srinivas
Published: November 2023

General Electric’s Renewable Energy business used to manually make annual sourcing and logistics plans to procure wind turbine towers from suppliers across the world and deliver them to customer sites. This process was time-consuming, cumbersome, suboptimal, and increased the cost of fulfilling customer demands. We developed an algorithm and a software tool to generate near-optimal towers’ sourcing and logistics plans, which minimized the total direct material and logistics costs incurred.
Castle Review
Authors: Barrett David C
Published: November 2023

Introduction: I produced the first edition of Cattle Review (then Cattle News) for the January 1999 edition of Livestock. This, the 158th edition (for some years there were 7 per annum), considers open access papers on Johne's disease, tuberculosis and digital dermatitis and marks 25 consecutive years!
Improving trimming and treatment skills through a collaborative approach
Authors: Pedersen Sara , Carter Tim
Published: November 2023

Strong vet–trimmer partnerships are crucial when it comes to tackling lameness, not only on farm but at national level. A collaborative partnership between the British Cattle Veterinary Association and the Cattle Hoof Care Standards Board to provide new foot trimming courses aims to provide evidence-based, accredited training at appropriate levels.
Efficacy of probiotics supplementation in amelioration of celiac disease symptoms and enhancement of immune system
Authors: Moawad Mostafa Hossam-Eldin , Alkhawaldeh Ibraheem M , Naswhan Abdulqadir J
Published: November 2023

Patients with celiac disease (CD) have a mucosal layer that is unable to regulate the gut microbiota, leaving the host vulnerable to dangerous infections and antigens. When compared to healthy people, this dysbiosis is marked by a decrease in intra- and intergeneric biodiversity, which demonstrates an imbalance between helpful bacteria and possibly harmful or proinflammatory species. The early gut microbiota is influenced by the genotype of newborns with the HLA-DQ2 haplotypes, and this may modify how gluten is handled in the intestinal lumen, polarize innate or adaptive immune responses, and result in glutensensitive enteropathy. The outcome of gluten digestion can vary depending on the composition of the intestinal gut bacteria and the partial conversion of gluten into peptides larger than ten amino acids in the small intestines, which can be immunogenic. In the small intestine, 114 different bacterial strains belonging to 32 different species have 27 of them exhibiting peptidolytic activity. Thus, the individual risk of developing a gluten-related illness is further influenced by microbial composition and gluten degrading capacity. The conclusion that lactobacilli and Bifidobacterium spp. may be used as a probiotic supplement in CD patients is based on their shared possession of the most extensive peptidolytic and proteolytic activity thought to be engaged in the breakdown of gluten among all potential bacterial genera present in the gut microbiota. In children with CD autoimmunity, daily oral dose of Lactobacillus. plantarum HEAL9 and Lactobacillus. paracasei 8700:2 was found to modify the peripheral immune response. Bifidobacterium. breve strains have demonstrated a beneficial effect on reducing pro-inflammatory cytokine TNF- production in CD children on gluten-free diets.
Emerging trends and hotspots of Nuclear factor erythroid 2-related factor 2 in nervous system diseases
Authors: Chang Xue-Qin , Xu Ling , Zuo Yi-Xuan , Liu Yi-Guo , Li Jia , Chi Hai-Tao
Published: November 2023

BACKGROUND

The Nuclear factor erythroid 2-related factor 2 (NRF2) transcription factor has attracted much attention in the context of neurological diseases. However, none of the studies have systematically clarified this field's research hotspots and evolution rules.

AIM

To investigate the research hotspots, evolution patterns, and future research trends in this field in recent years.

METHODS

We conducted a comprehensive literature search in the Web of Science Core Collection database using the following methods: (((((TS=(NFE2 L2)) OR TS=(Nfe2 L2 protein, mouse)) OR TS=(NF-E2-Related Factor 2)) OR TS=(NRF2)) OR TS=(NFE2L2)) OR TS=(Nuclear factor erythroid2-related factor 2) AND (((((((TS=(neurological diseases)) OR TS=(neurological disorder)) OR TS=(brain disorder)) OR TS=(brain injury)) OR TS=(central nervous system disease)) OR TS=(CNS disease)) OR TS=(central nervous system disorder)) OR TS=(CNS disorder) AND Language = English from 2010 to 2022. There are just two forms of literature available: Articles and reviews. Data were processed with the software Cite-Space (version 6.1. R6).

RESULTS

We analyzed 1884 articles from 200 schools in 72 countries/regions. Since 2015, the number of publications in this field has increased rapidly. China has the largest number of publications, but the articles published in the United States have better centrality and H-index. Among the top ten authors with the most published papers, five of them are from China, and the author with the most published papers is Wang Handong. The institution with the most articles was Nanjing University. To their credit, three of the top 10 most cited articles were written by Chinese scholars. The keyword co-occurrence map showed that "oxidative stress", "NRF2", "activation", "expression" and "brain" were the five most frequently used keywords.

CONCLUSION

Research on the role of NRF2 in neurological diseases continues unabated. Researchers in developed countries published more influential papers, while Chinese scholars provided the largest number of articles. There have been numerous studies on the mechanism of NRF2 transcription factor in neurological diseases. NRF2 is also emerging as a potentially effective target for the treatment of neurological diseases. However, despite decades of research, our knowledge of NRF2 transcription factor in nervous system diseases is still limited. Further studies are needed in the future.
Median arcuate ligament syndrome complicated with gallbladder stones: A case report
Authors: Dang Jun-Qiang , Wang Qing-Qiang , Yang Yan-Ling , Shang Lin , Bian Qi-Tian , Xiang Hong-Jun
Published: November 2023

BACKGROUND

Median arcuate ligament syndrome (MALS) is a rare disease caused by compression of the celiac trunk artery by the median arcuate ligament (MAL). It can cause symptoms of postprandial abdominal pain, weight loss, and nausea and vomiting.

CASE SUMMARY

A 55-year-old woman was admitted due to abdominal pain, nausea and vomiting. On admission, the patient presented with epigastric pain that worsened after eating, without signs of peritoneal irritation. Computed tomography angiography of the upper abdomen showed compression of the proximal segment of the abdominal trunk, local luminal stenosis with angular “fishhook” changes, which changed significantly during forceful inspiration and expiration; gallbladder stones; and multiple cysts in the liver. Abdominal duplex ultrasonography showed that peak systolic velocity was 352 cm/s. After diagnosis of MALS was confirmed, an arch ligament release procedure was performed. MALS has no specific symptoms and can be misdiagnosed as other abdominal diseases. Awareness of MALS should be improved to avoid misdiagnosis. The commonly used treatment option is MAL release and resection of the peripheral ganglion of the celiac trunk artery.

CONCLUSION

The diagnosis and treatment of MALS must be individualized, and MAL release is effective and provides immediate symptomatic relief.
Circumventing "Hostipitality": The Enduring Legacy of 19th-Century Choctaw Nation and Irish Solidarity
Authors: Gaillet Lynée Lewis
Published: November 2023

Abstract: The abiding legacy between the Choctaw Nation and Irish citizens stems from a small act of kindness in the 19th century. Following their forced migration during the 1830s, aptly remembered as the Trail of Tears, the Choctaw Nation donated $710 in 1847 ($26,468.37 in 2023 currency) to address Irish poverty resulting from the potato famine (Howe and Kirwan, xxvii). This act of benevolence established a cultural bond between the two groups—one that still thrives and has expanded to include other participants and recipients of their largesse.
Reason in Madness: Ariosto’s Ambiguous Irony between Truth and Morality
Authors: Casanova Elena
Published: November 2023

Abstract: Irony has always been a central focus of Ariosto scholarship: in particular, the interrelation between the endless flux of words and adventures that fill the Furioso , and the binary oppositions at the base of the poem has been considered a key ironic feature. Ariosto’s demiurgical distance is however not a sign of indifference: I argue that, while Ariosto’s irony transmits an estrangement from the traditional chivalric values, the author’s trust in the affirmative power of language and in its didactic function lies at the root of the Furioso ’s moral irony. Irony is, in fact, a vehicle for Ariosto’s ethical stance, but also a warning against the hypocrisy of courtly norms. First, I analyze the moral function of the Furioso ’s ironic narrator and Ariosto’s intimate relation to his audience, which thrives on complexity, difference, and multiplicity. I then look at the role that contradictions and (mis)quotations play within the poem’s ironic structure. Finally, I investigate how the Satire might represent the outer threshold of Ariosto’s irony. In fact, if in the Furioso Ariosto’s escapism could take shape thanks to the fantastic element, the Satire ’s ironic movement is revealed under a new, “barer” guise that walks a thin line between irony and moral satire.
The Secret
Authors: Strauss Liane
Published: November 2023

Abstract: In “The Secret” a poet returns home from a funeral and reflects on the ways another’s life is as mysterious as death.
A Pencil, and: Sky & Sky, and: Dust Motes
Authors: Swensen Cole
Published: November 2023

Abstract: These three poems are from a manuscript titled “Careen,” a collection of short prose poems often based on a faux- or specious-logic, at times veering (hence the title) toward the absurd, in an attempt—through the ridiculous, or at the very least, the unlikely—to retain some degree of optimism in spite of it all. And they are relentlessly optimistic, thinking that our only chance of effecting necessary change will be based on the strength gained from committing ourselves to all the astonishing beauty and intensity of the world we are threatening.
Acoustic characteristics of laser-induced plasmas from the forming dynamics perspective
Authors: Wu Wendong , Chai Shu , Zhou Yuegui
Published: November 2023

The acoustic signal has demonstrated its capabilities in assisting laser-induced breakdown spectroscopy (LIBS) measurements. In this study, the acoustic characteristics of laser-induced plasmas (LIPs) under different levels of energy deposition were analyzed, and their correlation with LIP forming dynamics was investigated. In the deposited energy space, two zones in the acoustic pressure and duration were observed, featuring a clear transition point in 100 mJ. The analysis based on self-emission spectra and images suggested that this transition is a result of the change in plasma forming dynamics. Above 100mJ, the plasma temperature and electron density were saturated; thus, any further increase in deposited energy only contributes to the plasma size. In this regime, the acoustic wave from the significantly elongated plasma no longer satisfied the ideal spherical assumption. The observation was also strengthened by the analysis in the frequency domain. Moreover, the correlation between acoustic and radiation signals was also changed significantly with plasma forming dynamics. This study offers a systematic analysis of LIP acoustic signals on the deposited energy space. The potential of using acoustic measurement to interpret the plasma forming dynamics was demonstrated, which could be beneficial for the successful implementations of acoustic-aided LIBS.
Tailored photoacoustic apertures with superimposed optical holograms
Authors: Howe Glenn A. , Tang Meng-Xing , Rowlands Christopher J.
Published: November 2023

A new method of generating potentially arbitrary photoacoustic wavefronts with optical holograms is presented. This method uses nanosecond laser pulses at 1064 nm that are split into four time-delayed components by means of a configurable multipass optical delay apparatus, which serves to map the pulses onto phase-delayed regions of a given acoustic wavefront. A single spatial light modulator generates separate holograms for each component, which are imaged onto a photoacoustic transducer comprised of a thermoelastic polymer. As a proof of concept of the broader arbitrary wavefront construction technique, the spatially- and temporally-modulated holograms in this study produce a phased array effect that enables beam steering of the resulting acoustic pulse. For a first experimental demonstration of the method, as verified by simulation, the acoustic beam is steered in four directions by around 5 degrees.
Integrated physical-layer secure visible light communication and positioning system based on polar codes
Authors: Fang Junbin , Pan Junxing , Huang Xia , Lin Jiajun , Jiang Canjian
Published: November 2023

Visible light communication (VLC) with physical-layer security can provide information-theoretic security for the optical wireless channel based on the characteristics of the channel instead of encryption algorithms and secret keys at application layer. Since precise location information of communication parties is crucial for estimating channel states and designing secure communication schemes, this paper proposes an integrated visible light communication and positioning system which provides triple functionalities of high-accuracy indoor positioning, physical-layer secure visible light communication, and flicker mitigation illumination. A heterogeneous signal hybrid line coding scheme is proposed for the transmitter to converge the high-speed communication data signals and the low-speed positioning data signals, and a hybrid heterogeneous signal extraction scheme is proposed for the receiver to separate the hybrid heterogeneous signals with a high-bandwidth photodetector and a low-pass complementary metal-oxide-semiconductor (CMOS) image sensor. Based on the positioning information and the communication scheme, a polar codes-based forward error correction coding scheme is designed to achieve physical-layer security and transmission reliability simultaneously. Numerical results show that the proposed system can reach a secrecy code rate of 0.76 for a single-input single-output indoor VLC channel and a transmission efficiency of 0.38 without perceivable flicker. Experimental results show that the proposed system can achieve an average positioning accuracy of 3.35 cm and decrease the bit error rate of a legitimate receiver to a near error-free level (lower than 10−7) while keeping the bit error rate of an eavesdropper at 0.4887 (nearly 0.5) with a transmission data rate of 1 Mbps, resulting in near-zero suppression of the eavesdropped information and a high secrecy capacity of 0.9994.
Elastoplastic contact model of pitch-based rough surface and its polishing characteristics
Authors: Li Fukun , Bai Yang , Hu HaiXiang , Li Longxiang , Li Lingzhong , Zhang Feng , Luo Xiao , Zhang Xuejun
Published: November 2023

Fused silica glass is widely used in optical systems, including astronomical telescopes, laser systems, optical communications, and the semiconductor industry. At the same time, the surface quality of the fused silica directly determines the performance and precision of the system. In order to analyze the microscopic surface interaction based on the basis of tribology, a roughness contact model of pitch and fused silica glass surfaces was established. Analyze the performance parameters of contact materials, surface roughness, and the relationship between load and contact area. Pitch materials with a higher plasticity index have a larger elastoplastic contact area with the fused silica surface during the polishing process. The experimental results demonstrate that the surface quality of the polished fused silica improves as the plasticity index of the pitch material increases. At the same time, judging from the PSD curve results, the polished surface of the No. 55 pitch on the spatial-frequency band curve (100-101/mm) is significantly lower than the other two brands of pitch. Additionally, the Ra value of the workpiece surface roughness reaches 0.091 nm. The results of this study provide important theoretical guidance for achieving full-diameter, full-frequency ultra-smooth polishing of large-diameter complex curved surfaces.
Optimal design for wavelength conversion with a configuration of walk-off compensation in free space in the nanosecond pulsed regime
Authors: Ohae Chiaki , Hasegawa Kenji , Nagano Masato , Tahara Soma , Katsuragawa Masayuki
Published: November 2023

On the basis of standard wavelength conversion by the use of angular phase matching of nonlinear optical crystals arranged in free space, applicable to a wide range of wavelengths and laser intensities, we both numerically and experimentally present an optimal design for achieving near-full energy conversion while maintaining good TEM00 mode property of fundamental laser radiation in the nanosecond regime.
Sub-diffraction optical beam lithography based on a center-non-zero depletion laser
Authors: Su Chenyi , Ding Chenliang , Yang Zhenyao , Cao Chun , Qiu Yiwei , Zhu Dazhao , Kuang Cuifang , Liu Xu
Published: November 2023

Photoinhibition (PI) mechanisms have been introduced in nanofabrication which allows breaking the diffraction limit by large factors. Donut-shaped laser is usually selected as a depletion beam to reduce linewidth, but the parasitic process has made the results of the experiment less than expected. As a result, the linewidth is difficult to achieve below 50 nm with 780 nm femtosecond and 532 nm continuous-wave lasers. Here, we propose a new, to the best of our knowledge, method based on a center-non-zero (CNZ) depletion laser to further reduce linewidth. By constructing a smaller zone of action under the condition of keeping the maximum depletion intensity constant, a minimum linewidth of 30 nm (λ / 26) was achieved. Two ways to construct CNZ spots were discussed and experimented, and the results show the advantages of our method to reduce the parasitic process to further improve the writing resolution.
Improving the resolution of Fourier ptychographic imaging using an a priori neural network
Authors: Sha Junting , Qiu Wenmao , He Guannan , Luo Zhi , Huang Bo
Published: November 2023

In this paper, we propose a dual-structured prior neural network model that independently restores both the amplitude and phase image using a random latent code for Fourier ptychography (FP). We demonstrate that the inherent prior information within the neural network can generate super-resolution images with a resolution that exceeds the combined numerical aperture of the FP system. This method circumvents the need for a large labeled dataset. The training process is guided by an appropriate forward physical model. We validate the effectiveness of our approach through simulations and experimental data. The results suggest that integrating image prior information with system-collected data is a potentially effective approach for improving the resolution of FP systems.
Sparse single-pixel imaging via optimization in nonuniform sampling sparsity
Authors: Yan Rong , Li Daoyu , Zhan Xinrui , Chang Xuyang , Yan Jun , Guo Pengyu , Bian Liheng
Published: November 2023

Reducing the imaging time while maintaining reconstruction accuracy remains challenging for single-pixel imaging. One cost-effective approach is nonuniform sparse sampling. The existing methods lack intuitive and intrinsic analysis in sparsity. The lack impedes our comprehension of the form’s adjustable range and may potentially limit our ability to identify an optimal distribution form within a confined adjustable range, consequently impacting the method’s overall performance. In this Letter, we report a sparse sampling method with a wide adjustable range and define a sparsity metric to guide the selection of sampling forms. Through a comprehensive analysis and discussion, we select a sampling form that yields satisfying accuracy. These works will make up for the existing methods’ lack of sparsity analysis and help adjust methods to accommodate different situations and needs.
Nonlinear optical properties and ultrafast carrier dynamics of ultrathin ReSe2
Authors: Mao Yu , Wang Hongqiang , Kislyakov Ivan , Wang Zixin , Dong Ningning , Wang Jun
Published: November 2023

Rhenium diselenide (ReSe2) has shown great application potential in the field of optical devices because of its excellent optoelectronic properties. In this study, we systematically investigated the nonlinear optical absorption properties of mono- and bi-layer ReSe2 and the ultrafast carrier dynamics process in the ultraviolet to near-infrared spectral range as the essential foundational groundwork for harnessing the potential of ultrathin ReSe2-based optoelectronic devices. We found that ReSe2 has excellent nonlinear absorption performance and a low saturation absorption intensity that is better than that of many semiconductor materials. Meanwhile, pump–probe and transient absorption technology revealed the underlying dynamic mechanisms, including bandgap renormalization and Auger recombination. This study can broaden the horizons of material science and propel the development of different applications of ReSe2.
Design of cost-effective environment-responsive nanoacoustic devices based on mesoporous thin films
Authors: Cardozo de Oliveira Edson R. , Vensaus Priscila , Soler-Illia Galo J. A. A. , Lanzillotti-Kimura Norberto Daniel
Published: November 2023

Gigahertz acoustic resonators have the potential to advance data processing and quantum communication. However, they are expensive and lack responsiveness to external stimuli, limiting their use in sensing applications. In contrast, low-cost nanoscale mesoporous materials, known for their high surface-to-volume ratio, have shown promise in various applications. We recently demonstrated that mesoporous silicon dioxide (SiO2) and titanium dioxide (TiO2) thin layers can support coherent acoustic modes in the 5 to 100 GHz range. In this study, we propose a new method for designing tunable acoustic resonators using mesoporous thin films on acoustic distributed Bragg reflectors. By simulating the infiltration of the pores with water, we show that the material’s properties could be altered and achieve tunability in the acoustic resonances. We present four device designs and use simulations to predict resonators with Q-factors up to 1500. We also observe that the resonant frequency and intensity show a linear response to water infiltrated in the mesopores, with a tunability of up to 60%. Our platform offers a unique opportunity to design cost-effective nanoacoustic sensing and reconfigurable optoacoustic nanodevices.
Carbon dioxide regulates cholesterol levels through SREBP2
Authors: Bolshette Nityanand , Ezagouri Saar , Dandavate Vaishnavi , Karavaeva Iuliia , Golik Marina , Wang Hu , Espenshade Peter J. , Osborne Timothy F. , Han Xianlin , Asher Gad
Published: November 2023

In mammals, O2 and CO2 levels are tightly regulated and are altered under various pathological conditions. While the molecular mechanisms that participate in O2 sensing are well characterized, little is known regarding the signaling pathways that participate in CO2 signaling and adaptation. Here, we show that CO2 levels control a distinct cellular transcriptional response that differs from mere pH changes. Unexpectedly, we discovered that CO2 regulates the expression of cholesterogenic genes in a SREBP2-dependent manner and modulates cellular cholesterol accumulation. Molecular dissection of the underlying mechanism suggests that CO2 triggers SREBP2 activation through changes in endoplasmic reticulum (ER) membrane cholesterol levels. Collectively, we propose that SREBP2 participates in CO2 signaling and that cellular cholesterol levels can be modulated by CO2 through SREBP2.
The activity of engrailed imaginal disc enhancers is modulated epigenetically by chromatin and autoregulation
Authors: Cheng Yuzhong , Chan Fountane , Kassis Judith A.
Published: November 2023

engrailed (en) encodes a homeodomain transcription factor crucial for the proper development of Drosophila embryos and adults. Like many developmental transcription factors, en expression is regulated by many enhancers, some of overlapping function, that drive expression in spatially and temporally restricted patterns. The en embryonic enhancers are located in discrete DNA fragments that can function correctly in small reporter transgenes. In contrast, the en imaginal disc enhancers (IDEs) do not function correctly in small reporter transgenes. En is expressed in the posterior compartment of wing imaginal discs; in contrast, small IDE-reporter transgenes are expressed mainly in the anterior compartment. We found that En binds to the IDEs and suggest that it may directly repress IDE function and modulate En expression levels. We identified two en IDEs, O and S. Deletion of either of these IDEs from a 79kb HA-en rescue transgene (HAen79) caused a loss-of-function en phenotype when the HAen79 transgene was the sole source of En. In contrast, flies with a deletion of the same IDEs from an endogenous en gene had no phenotype, suggesting a resiliency not seen in the HAen79 rescue transgene. Inserting a gypsy insulator in HAen79 between en regulatory DNA and flanking sequences strengthened the activity of HAen79, giving better function in both the ON and OFF transcriptional states. Altogether our data suggest that the en IDEs stimulate expression in the entire imaginal disc, and that the ON/OFF state is set by epigenetic memory set by the embryonic enhancers. This epigenetic regulation is similar to that of the Ultrabithorax IDEs and we suggest that the activity of late-acting enhancers in other genes may be similarly regulated.
Livestock, pathogens, vectors, and their environment: A causal inference-based approach to estimating the pathway-specific effect of livestock on human African trypanosomiasis risk
Authors: Meisner Julianne , Kato Agapitus , Lemerani Marshall , Mwamba Miaka Erick , Ismail Taban Acaga , Wakefield Jonathan , Rowhani-Rahbar Ali , Pigott David M. , Mayer Jonathan , Rabinowitz Peter M.
Published: November 2023

Livestock are important reservoirs for many zoonotic diseases, however the effects of livestock on human and environmental health extend well beyond direct disease transmission. In this retrospective ecological cohort study we use pre-existing data and the parametric g-formula, which imputes potential outcomes to quantify mediation, to estimate three hypothesized mechanisms by which livestock can influence human African trypanosomiasis (HAT) risk: the reservoir effect, where infected cattle and pigs are a source of infection to humans; the zooprophylactic effect, where preference for livestock hosts exhibited by the tsetse fly vector of HAT means that their presence protects humans from infection; and the environmental change effect, where livestock keeping activities modify the environment in such a way that habitat suitability for tsetse flies, and in turn human infection risk, is reduced. We conducted this study in four high burden countries: at the point level in Uganda, Malawi, and Democratic Republic of Congo (DRC), and at the county level in South Sudan. Our results indicate cattle and pigs play a reservoir role for the rhodesiense form (rHAT) in Uganda (rate ratio (RR) 1.68, 95% CI 0.84, 2.82 for cattle; RR 2.16, 95% CI 1.18, 3.05 for pigs), however zooprophylaxis outweighs this effect for rHAT in Malawi (RR 0.85, 95% CI 0.68, 1.00 for cattle, RR 0.38, 95% CI 0.21, 0.69 for pigs). For the gambiense form (gHAT) we found evidence that pigs may be a competent reservoir (RR 1.15, 95% CI 0.92, 1.72 in Uganda; RR 1.25, 95% CI 1.11, 1.42 in DRC). Statistical significance was reached for rHAT in Malawi (pigs and cattle) and Uganda (pigs only) and for gHAT in DRC (pigs and cattle). We did not find compelling evidence of an environmental change effect (all effect sizes close to 1).
Techniques to assess reproductive status in adult female American alligators (Alligator mississippiensis) using laparoscopic examination
Authors: Flint Mark , Flint Jaylene B. , Miller Jeffrey D.
Published: November 2023

This protocol describes a minimally invasive surgical technique and approach to successfully examine the gonads of live female American alligators as part of a reproductive examination used in conservation medicine and biology. Best practices are based on examination of over 80 American alligators in the last two years adapting principles derived from other reptilian megafauna species. This protocol is designed for appropriately qualified veterinarians and biologists working in the field. We show likely reproductive tract presentations with respect to breeding status and environmental cues to help guide interpretation of observations. The laparoscopic approach and findings presented here provide tools to safely clinically examine animals in a welfare-oriented way that will advance our understanding of crocodilian reproduction. This technique has not previously been described in this species.
A systematic literature review: Real-time 3D reconstruction method for telepresence system
Authors: Fadzli Fazliaty Edora , Ismail Ajune Wanis , Abd Karim Ishigaki Shafina
Published: November 2023

Real-time three-dimensional (3D) reconstruction of real-world environments has many significant applications in various fields, including telepresence technology. When depth sensors, such as those from Microsoft’s Kinect series, are introduced simultaneously and become widely available, a new generation of telepresence systems can be developed by combining a real-time 3D reconstruction method with these new technologies. This combination enables users to engage with a remote person while remaining in their local area, as well as control remote devices while viewing their 3D virtual representation. There are numerous applications in which having a telepresence experience could be beneficial, including remote collaboration and entertainment, as well as education, advertising, and rehabilitation. The purpose of this systematic literature review is to analyze the recent advances in 3D reconstruction methods for telepresence systems and the significant related work in this field. Next, we determine the input data and the technological device employed to acquire the input data, which will be utilized in the 3D reconstruction process. The methods of 3D reconstruction implemented in the telepresence system as well as the evaluation of the system, have been extracted and assessed from the included studies. Through the analysis and summarization of many dimensions, we discussed the input data used for the 3D reconstruction method, the real-time 3D reconstruction methods implemented in the telepresence system, and how to evaluate the system. We conclude that real-time 3D reconstruction methods for telepresence systems have progressively improved over the years in conjunction with the advancement of machines and devices such as Red Green Blue-Depth (RGB-D) cameras and Graphics Processing Unit (GPU).
Novel breath biomarkers identification for early detection of hepatocellular carcinoma and cirrhosis using ML tools and GCMS
Authors: Ain Nazir Noor ul , Shaukat Muhammad Haroon , Luo Ray , Abbas Shah Rukh
Published: November 2023

According to WHO 2019, Hepatocellular carcinoma (HCC) is the fourth highest cause of cancer death worldwide. More precise diagnostic models are needed to enhance early HCC and cirrhosis quick diagnosis, treatment, and survival. Breath biomarkers known as volatile organic compounds (VOCs) in exhaled air can be used to make rapid, precise, and painless diagnoses. Gas chromatography and mass spectrometry (GCMS) are utilized to diagnose HCC and cirrhosis VOCs. In this investigation, metabolically generated VOCs in breath samples (n = 35) of HCC, (n = 35) cirrhotic, and (n = 30) controls were detected via GCMS and SPME. Moreover, this study also aims to identify diagnostic VOCs for distinction among HCC and cirrhosis liver conditions, which are most closely related, and cause misleading during diagnosis. However, using gas chromatography-mass spectrometry (GC-MS) to quantify volatile organic compounds (VOCs) is time-consuming and error-prone since it requires an expert. To verify GC-MS data analysis, we present an in-house R-based array of machine learning models that applies deep learning pattern recognition to automatically discover VOCs from raw data, without human intervention. All-machine learning diagnostic model offers 80% sensitivity, 90% specificity, and 95% accuracy, with an AUC of 0.9586. Our results demonstrated the validity and utility of GCMS-SMPE in combination with innovative ML models for early detection of HCC and cirrhosis-specific VOCs considered as potential diagnostic breath biomarkers and showed differentiation among HCC and cirrhosis. With these useful insights, we can build handheld e-nose sensors to detect HCC and cirrhosis through breath analysis and this unique approach can help in diagnosis by reducing integration time and costs without compromising accuracy or consistency.