bluuebunny/crossref_metadata_2025 huggingface dataset:
The Ideal Diet for Humans to Sustainably Feed the Growing Population – Review, Meta-Analyses, and Policies for Change
Authors: Goldfarb Galit , Sela Yaron
Published: June 2023

Introduction: As of now, no study has combined research from different sciences to determine the most suitable diet for humans. This issue is urgent due to the predicted population growth, the effect of this on the environment, and the deterioration of human health and associated costs.

Methods: A literature review determined whether an optimal diet for humans exists and what such a diet is, followed by six meta-analyses. The standard criteria for conducting meta-analyses of observational studies were followed. A review of literature reporting Hazard Ratios with a 95% confidence interval for red meat intake, dairy intake, plant-based diet, fiber intake, and serum IGF-1 levels were extracted to calculate effect sizes.

Results: Results calculated using NCSS software show that high meat consumption increases mortality probability by 18% on average and increases diabetes risk by 50%. Plant-based and high-fiber diets decrease mortality by 15% and 20% respectively (p < .001). Plant-based diets decreased diabetes risk by 27%, and dairy consumption (measured by increased IGF-1 levels) increased cancer probability by 48% (p < 0.01). A vegetarian or Mediterranean diet was not found to decrease the probability of heart disease. A vegetarian diet can be healthy or not, depending on the foods consumed. A Mediterranean diet with high quantities of meat and dairy products will not produce the health effects desired. The main limitations of the study were that observational studies were heterogeneous and limited by potential confounders.

Discussion: The literature and meta-analyses point to an optimal diet for humans that has followed our species from the beginnings of humankind. The optimal diet is a whole food, high fiber, low-fat, 90+% plant-based diet. This diet allowed humans to become the most developed species on Earth. To ensure people’s nutritional needs are met healthily and sustainably, governmental dietary interventions are necessary.
Decaffeinated coffee and green tea extract inhibit foam cell atherosclerosis by lowering inflammation and improving cholesterol influx/efflux balance through upregulation of PPARγ and miR-155
Authors: Rachmawati Ermin , Rohman Mohammad Saifur , Sargowo Djanggan , Kalsum Umi , Lyrawati Diana , Lukitasari Mifetika
Published: June 2023

Background: Foam cells, the markers of early atherosclerosis and characterise the advanced atherosclerotic plaque, are stimulated by inflammation due to the excess of lipid in macrophages. The combination of decaffeinated coffee and green tea extract (DCGTE) has been suggested to have a role in foam cell inhibition.

Objective: to investigate the role of DCGTE against foam cell formation, through modulation of the inflammation process and cholesterol metabolism in macrophage colony stimulating factor (M-CSF) and oxidized low-density lipoprotein (oxLDL)-exposed macrophages.

Methods: Coffee and green tea were extracted by filtration and infusion respectively. Both of coffee and green tea underwent decaffeination using active carbon and blanching methods, respectively. Raw 264.7 Cells were administered with 160/160 and 320/320 μg/ml of DCGTE. Foam cell formation was observed using a light microscope after staining with Oil Red O (ORO), and quantified with ELISA. The expression of cluster differentiation 36 (CD36) ( lipid influx) and ATP binding cassette transporter A1 (ABCA1) ( cholesterol efflux) were determined through immunofluorescence. Tumor Necrosis Factor α (TNFα) and Interleukin10 (IL10) were quantified with ELISA. Peroxisome proliferator activated response γ (PPARγ) expression and activity were assessed with Polymerase Chain Reaction (PCR) and ELISA, respectively. The expression of microRNA 155 (miR-155) was examined using qPCR.

Results: DCGTE at the above concentrations tended to reduce foam cell numbers, significantly inhibited lipid accumulation (p=0.000), reduced CD36 expression (p=0.000) and TNFα secretion (p=0.000) in Raw264.7 exposed to M-CSF 50 ng/ml and oxLDL 50 μg/ml.  The PPARγ expression (p=0.000), PPARγ activity (p=0.001), ABCA1 (p=0.002), miR-155 relative expression (p=0.000), and IL10 production (p=0.000) also increased in DCGTE groups.

Conclusion: DCGTE lowered foam cell possibly through attenuation of the inflammatory process and improvement of lipid/efflux mechanisms via upregulation of PPARγ and miR-155 in M-CSF and oxLDL-stimulated Raw264.7 cells.  Our results suggest DCGTE might help to prevent atherosclerosis-based diseases.
Investigating antiquities trafficking with generative pre-trained transformer (GPT)-3 enabled knowledge graphs: A case study
Authors: Graham Shawn , Yates Donna , El-Roby Ahmed
Published: June 2023

Background: There is a wide variety of potential sources from which insight into the antiquities trade could be culled, from newspaper articles to auction catalogues, to court dockets, to personal archives, if it could all be systematically examined. We explore the use of a large language model, GPT-3, to semi-automate the creation of a knowledge graph of a body of scholarship concerning the antiquities trade.

Methods: We give GPT-3 a prompt guiding it to identify knowledge statements around the trade. Given GPT-3’s understanding of the statistical properties of language, our prompt teaches GPT-3 to append text to each article we feed it where the appended text summarizes the knowledge in the article. The summary is in the form of a list of subject, predicate, and object relationships, representing a knowledge graph. Previously we created such lists by manually annotating the source articles. We compare the result of this automatic process with a knowledge graph created from the same sources via hand. When such knowledge graphs are projected into a multi-dimensional embedding model using a neural network (via the Ampligraph open-source Python library), the relative positioning of entities implies the probability of a connection; the direction of the positioning implies the kind of connection. Thus, we can interrogate the embedding model to discover new probable relationships. The results can generate new insight about the antiquity trade, suggesting possible avenues of research.

Results: We find that our semi-automatic approach to generating the knowledge graph in the first place produces comparable results to our hand-made version, but at an enormous savings of time and a possible expansion of the amount of materials we can consider.

Conclusions: These results have implications for working with other kinds of archaeological knowledge in grey literature, reports, articles, and other venues via computational means.
The genome sequence of the Cinnabar Moth, Tyria jacobaeae (Linnaeus, 1758)
Authors: Boyes Douglas , Sivell Olga , Holland Peter W.H. ,   University of Oxford and Wytham Woods Genome Acquisition Lab,   Natural History Museum Genome Acquisition Lab,   Darwin Tree of Life Barcoding collective,   Wellcome Sanger Institute Tree of Life programme,   Wellcome Sanger Institute Scientific Operations: DNA Pipelines collective,   Tree of Life Core Informatics collective,   Darwin Tree of Life Consortium
Published: June 2023

We present a genome assembly from an individual male Tyria jacobaeae (the Cinnabar Moth; Arthropoda; Insecta; Lepidoptera; Erebidae). The genome sequence is 589.7 megabases in span. Most of the assembly is scaffolded into 31 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 15.74 kilobases in length.
Political text: psycholinguistic analysis of the impact on the electorate
Authors: Repina Ekaterina
Published: June 2023

The monograph is an analysis of Russian propaganda and political materials from the late 1990s to the present. The work is based on a scientific study conducted in the 1990s-2000s within the framework of psycholinguistics and a communicative approach and included an experimental assessment of the impact of political texts on the recipient of information, as well as an analysis of the linguistic means of this impact.
It is intended for political consultants, political technologists, staff of the apparatus of political parties and social movements. It can also be used by university teachers and students receiving education in the field of political science, journalism, public relations, linguistics, psychology, sociology.
Generation of a vector conventional soliton via a graphene oxide saturable absorber
Authors: Mei Chao , Duan Lina , Chang Sansan , Guo Xinyu , Yu Jia
Published: June 2023

We have experimentally observed an ultrashort conventional vector soliton in an erbium-doped fiber laser. The few-layered graphene oxide (GO) is used as a saturable absorber (SA). It is found that the saturable absorption characteristic of GO is polarization independent. Therefore, vector solitons can be obtained without polarization control by using such SA. By using a polarization beam splitter to split the mode-locked pulse obtained in the oscillator, two orthogonal polarization vector solitons with equal intensity and consistent characteristics can be obtained. It demonstrates that the initial soliton consists of two orthogonal polarization components. It is worth noting that these two orthogonal polarization component solitons improve the signal-to-noise ratio (SNR) of 3 dB compared with the initial soliton. The improvement in SNR is very significant and cannot be neglected. This phenomenon has not been reported before, to our knowledge. In addition, the conventional soliton generated by this mode-locked laser has a central wavelength of 1559 nm with 1.1 ps pulse duration. The mode-locking state of this laser can be self-started. After mode locking, the environmental stability is excellent. The experimental results indicate that GO as a broadband SA has great potential and application prospects in the field of vector soliton generation.
Single-copy entanglement purification for Greenberger–Horne–Zeilinger states
Authors: Yan Pei-Shun , Zhou Lan , Sheng Yu-Bo
Published: June 2023

A multiparticle entangled state is an indispensable resource in quantum information processing. However, the inherent noise in quantum channels may degrade the maximally entangled state to a mixed entangled state. An entanglement purification protocol (EPP) is a powerful tool to distill high-quality entanglement from low-quality entanglement. Conventional multiparticle EPPs (MEPPs) mainly focus on two noisy copies. In this paper, we investigate a single-copy MEPP (SCMEPP) in linear optics that requires only a pair of hyperentanglements. Specifically, we first purify the bit-flip errors for three-particle polarization Greenberger–Horne–Zeilinger (GHZ) states at the cost of time-bin entanglement, and then an analysis of correcting the phase-flip errors is carried out. Additionally, we extend this SCMEPP into purification for arbitrary multiparticle GHZ states. Moreover, we discuss the discarding components that have been regarded as failure in conventional two-copy MEPPs, and they still have entanglement if the fidelities of the initial states satisfy specific conditions. This can be reused to distill high-quality entanglement, therefore increasing the efficiency of the SCMEPP, which may have potential application to realize high-efficiency long-distance quantum communication.
Subwavelength thickness characterization of curved dielectric films exploiting spatially structured entangled photons
Authors: Ataç Enes , Dinleyici Mehmet Salih
Published: June 2023

Precise determination of thin dielectric film optical properties is a critical issue for fiber optic sensor technologies. However, conventional methods for the optical characterization of these films not only are generally complex and tedious processes on curved surfaces but also require well-calibrated and overly sophisticated devices. We, on the other hand, propose a novel and practical quantum-based phase diffraction scheme to characterize the thickness of ultra-thin transparent dielectric films coated on an optical fiber beyond the classical diffraction limits in this paper. The approach is implemented by evaluating the effect of thickness variations on the highly visible two-photon diffraction pattern’s zero crossings and amplitudes. The mathematical model and numerical simulations contribute to a better understanding of how the spatially structured entangled photons improve thickness precision with the help of intensity correlations and a confocal aperture. To prove the impact of the proposed system, it is compared with the classical phase diffraction method in the literature via simulations. According to the results, the thickness of the transparent dielectric films can be accurately estimated below one-twentieth of the wavelength of interest.
Temporal soliton dynamics of synchronised ultrafast fibre lasers
Authors: Zheng Jiancheng , Li Diao , Cui Xiaoqi , Liu Peng , Zhang Qiang , Zhu Zhiwei , Yang Song , Zhang Yusheng , Sun Jiaxing , Chen Xianfeng , Yang Haima , Kauppinen Esko I. , Sun Zhipei
Published: June 2023

Synchronised ultrafast soliton lasers have attracted great research interest in recent decades. However, there is a lack of comprehensive understanding regarding the buildup mechanism of synchronised pulses. Here, we report a dynamic analysis of independent and synchronised solitons buildup mechanisms in synchronised ultrafast soliton lasers. The laser comprises an erbium-doped fibre cavity and a thulium-doped fibre cavity bridged with a common arm. Pulses operating at two different wavelengths formed in the cavities are synchronised by cross-phase modulation-induced soliton correlation in the common fibre arm. We find that the whole buildup process of the thulium-doped fibre laser successively undergoes five different stages: continuous wave, relaxation oscillation, quasi-mode-locking, continuous wave mode-locking and synchronised mode-locking. It is found that the starting time of the synchronised solitons is mainly determined by the meeting time of dual-color solitons. Our results will further deepen the understanding of dual-color synchronised lasers and enrich the study of complex nonlinear system dynamics.
Time/frequency-domain characterization of a mid-IR DFG frequency comb via two-photon and heterodyne detection
Authors: Gabbrielli Tecla , Insero Giacomo , De Regis Michele , Corrias Nicola , Galli Iacopo , Mazzotti Davide , Bartolini Paolo , Hyun Huh Jeong , Cleff Carsten , Kastner Alexander , Holzwarth Ronald , Borri Simone , Consolino Luigi , De Natale Paolo , Cappelli Francesco
Published: June 2023

Mid-infrared frequency combs are nowadays well-appreciated sources for spectroscopy and frequency metrology. Here, a comprehensive approach for characterizing a difference-frequency-generated mid-infrared frequency comb (DFG-comb) both in the time and in the frequency domain is presented. An autocorrelation scheme exploiting mid-infrared two-photon detection is used for characterizing the pulse width and to verify the optimal compression of the generated pulses reaching a pulse duration (FWHM) as low as 196 fs. A second scheme based on mid-infrared heterodyne detection employing two independent narrow-linewidth quantum cascade lasers (QCLs) is used for frequency-narrowing the modes of the DFG-comb down to 9.4 kHz on a 5-ms timescale.
Advantages of one- and two-photon light in inverse scattering
Authors: Avetisyan H. , Mkrtchian V. , Allahverdyan A. E.
Published: June 2023

We study an inverse scattering problem in which the far-field spectral cross correlation functions of scattered fields are used to determine the unknown dielectric susceptibility of the scattering object. One-photon states for the incident field can resolve (at 100% visibility) twice as many Fourier components of the susceptibility compared with the (naïve) Rayleigh estimate, provided that the measurement is performed in the back-scattering regime. Coherent states are not capable of reaching this optimal resolution (or do so with negligible visibility). Using two-photon states improves upon the one-photon resolution, but the improvement (at 100% visibility) is smaller than twice, and it demands prior information on the object. This improvement can also be realized via two independent laser fields. The dependence on the prior information can be decreased (but not eliminated completely) upon using entangled states of two photons.
Modal phase-locking in multimode nonlinear optical fibers
Authors: Mangini Fabio , Ferraro Mario , Sun Yifan , Gervaziev Mikhail , Parra-Rivas Pedro , Kharenko Denis S. , Couderc Vincent , Wabnitz Stefan
Published: June 2023

Spatial beam self-cleaning, a manifestation of the Kerr effect in graded-index multimode fibers, involves a nonlinear transfer of power among modes, which leads to robust bell-shaped output beams. The resulting mode power distribution can be described by statistical mechanics arguments. Although the spatial coherence of the output beam was experimentally demonstrated, there is no direct study of modal phase evolutions. Based on a holographic mode decomposition method, we reveal that nonlinear spatial phase-locking occurs between the fundamental and its neighboring low-order modes, in agreement with theoretical predictions. As such, our results dispel the current belief that the spatial beam self-cleaning effect is the mere result of a wave thermalization process.
Femtosecond-laser-inscribed Bragg grating in hollow-core fiber for highly sensitive optofluidic sensing
Authors: Cheng Wei , Liu Shuhui , Zhao Shengguo , Li Litong
Published: June 2023

An optofluidic sensor based on a Bragg grating in hollow-core fiber (HCF) is experimentally demonstrated. The grating is inscribed into the HCF by femtosecond laser illumination through a phase mask. Periodic index modulation is introduced into the silica material surrounding the hollow core, causing cladding mode resonance, and multiple reflection peaks are observed in the grating spectrum. These reflection peaks later shift to longer wavelengths when high-index liquid is infiltrated into the HCF. The new reflection peak results from the backward coupling of the liquid core mode of the waveguide, the mode field of which overlaps with the grating modulation surrounding the liquid core. The resonant wavelength of the liquid-core fiber grating increases with the index value of the infiltrating liquid, and optofluidic refractive index sensing is realized with the device. The highest refractive index sensitivity, 1117 nm/RIU, is obtained experimentally in the index range of 1.476−1.54. The infiltrated hollow-core fiber Bragg grating also exhibits high temperature sensitivity due to the high thermal-optic coefficient of the liquid, and a sensitivity of −301 pm/°C is achieved in the temperature range of 25°C to 60°C.
Photonic molecule state transition by collision
Authors: Willms Stephanie , Melchert Oliver , Bose Surajit , Babushkin Ihar , Morgner Uwe , Demircan Ayhan
Published: June 2023

We investigate the impact of collisions with two-frequency photonic molecules aiming to observe internal dynamic behavior and challenge their strong robustness. Versatile interaction scenarios show intriguing state changes expressed through modifications of the resulting state such as temporal compression and unknown collision-induced spectral tunneling. These processes show potential for efficient coherent supercontinuum generation and all-optical manipulation.
Variable ratio blue/red upconversion in Yb3+-Tm3+ codoped fluorosilicate glasses
Authors: Wang Xin , Tian Ke , Zhao Haiyan , Zhao Xiaotong , Zhang Zhi , Yu Jin , Liu Dejun , Brambilla Gilberto , Wang Pengfei
Published: June 2023

Simultaneous blue-red emission in a fiber pumped by a single wavelength source is perceived as a great challenge because of the large energy difference of the emitted photons. This Letter reports the dependence of the blue-to-red upconversion (UC) emission ratio in Yb3+-Tm3+ codoped fluorosilicate glasses (FSGs) under the excitation of a 980-nm laser on the host glass silica content. Photoluminescence spectra and SEM-EDS are used to clarify the UC mechanism, indicating that the probability of the cross-relaxation (CR) process 1G4 + 3F2→3H6 + 3F4 is key to the dominance of the blue or red emissions. This research can provide a new platform for variable UC luminescence.
Plasmon-enhanced deep ultraviolet Micro-LED arrays for solar-blind communications
Authors: Zhang Siyao , He Rui , Duo Yiwei , Chen Renfeng , Wang Ligang , Wang Junxi , Wei Tongbo
Published: June 2023

Localized surface plasmon resonance (LSPR)-enhanced deep ultraviolet (DUV) Micro-light emitting diodes (Micro-LEDs) using Al nanotriangle arrays (NTAs) are reported for improving the −3 dB modulation bandwidth. Through self-assembled nanospheres, the high-density Al NTAs arrays are transferred into the designated p-AlGaN region of the Micro-LEDs, realizing the effect of LSPR coupling. A 2.5-fold enhancement in photoluminescence (PL) intensity is demonstrated. Combined with the PL intensity ratio at 300 K and 10 K, internal quantum efficiency (IQE) may be increased about 15–20% by the plasmonic effect and the carrier lifetime decreases from 1.15 ns to 0.82 ns, suggesting that LSPR accelerates the spontaneous emission rate. Resulting from the improvement of the IQE, the electroluminescence intensity of Micro-LED arrays with LSPR is obviously increased. Meanwhile, the −3 dB bandwidth of 6 × 6 Micro-LED arrays is increased from 180 MHz to 300 MHz at a current density of 200 A/cm2. A potential way is proposed to further increase both the IQE and the modulation bandwidth of DUV Micro-LEDs.
Super-resolution and apodization with discrete adaptive optics
Authors: Cagigal M. P. , Fuentes A. , Canales V. F. , Valle P. J. , Cagigas M. A. , Castellanos O.
Published: June 2023

High-resolution imaging is of great importance in various fields. The use of pupil phase-only filters (PPF) exceeds the diffraction limit of the imaging system in a simple way. When dealing with distorted wavefronts, however, PPF require that aberrations be compensated for. In this paper, we introduce a novel technique consisting of the use of discrete adaptive optics with PPFs so that the compensating device implements the PPF at the same time. Analysis of the theory for point spread function reshaping using PPFs has enabled us to develop a new approach to characterizing apodizing filters. A validation experiment has been carried out, the first of its kind to our knowledge, in which a number of PPFs were combined with two levels of compensation. Our experimental results are discussed.
High frequency characterization of PZT thin-films deposited by chemical solution deposition on SOI for integrated high speed electro-optic modulators
Authors: Feutmba Gilles F. , da Silva Leandro , Singh Nishant , Breyne Laurens , De Geest Kobe , George John Puthenparampil , Bauwelinck Johan , Van Thourhout Dries , Yin Xin , Beeckman Jeroen
Published: June 2023

The increasing demand for high data rates and low power consumption puts silicon photonics at the edge of its capabilities. The heterogeneous integration of optical ferro-electric materials on silicon enhances the functionality of the silicon on insulator (SOI) platform to meet these demands. Lead zirconate titanate (PZT) thin films with a large Pockels coefficient and good optical quality can be directly integrated on SOI waveguides for fast electro-optic modulators. In this work, the relative permittivity and dielectric loss of PZT thin films deposited by chemical solution deposition on SOI substrates are analyzed at high frequencies. We extract ε
r
=1650−2129 and tan (δ) = 0.170 − 0.209 for the PZT thin films in the frequency range 1-67GHz. We show the possibility of achieving bandwidths beyond 60GHz via a Mach-Zehnder modulator with V
π
 = 7V, suitable for next generation data communication systems.
Highly luminescent ultra-thin films with rare earth for plasmonic applications
Authors: Munga J. , Yang C. , Rab Md A. , Shahbazyan T. V. , Durach M. , Noginov M. A. , Noginova N.
Published: June 2023

Amphiphilic complexes with luminescent rare earth metal ions suitable for Lanmuir-Blodgett (LB) deposition have been synthesized. LB monolayers with closely packed Eu complexes deposited directly on silver demonstrate significant far-field emission in contrast to the theoretical predictions of full quenching. Angular radiation and polarization patterns of the electric and magnetic dipole emission of Eu3+ point to a high excitation efficiency of surface plasmon polaritons. Different luminescent behavior of closely packed emitters in comparison to diluted systems is tentatively attributed to the collective state of emitters in LB layers formed via near-field coupling with surface plasmons.
Multifunctional plasmonic gates using the effect of voltage on the surface plasmons frequency change
Authors: jafargholikhani fatemeh , Kashaninia Alireza , Sabbaghi-Nadooshan Reza
Published: June 2023

Considering the benefits of plasmonic technology in reducing the scattering limit on bends and low losses, as well as the small size of the element, the development of this technology has accelerated. In this paper, the effect of voltage application on changing the frequency of surface plasmons is investigated. By applying an external voltage to the metal plates and creating a magnetic field, the density of the electrons on the metal surface changes; thus, surface plasmons resonance frequency shifts. To this end, a multifunctional plasmonic gate with a dimension of 95 nm × 95 nm was designed and
simulated to evaluate this effect. This structure is suitable for use as AND, NOR, NOT, XOR, and NAND gates. The contrast ratio between the change of state from logic "0" to logic "1" is approximately 29 dB, and the transfer ratio (transmittance ratio) of output in logic "1" is over 85%. The proposed device has low dimensions, a high contrast ratio, and a high transmittance ratio. This device uses four gates: AND, NOR, NOT, XOR, and NAND, which can be achieved in plasmonic integrated circuits with the wavelength division multiplexing (WDM) technique.
Modeling the sequence dependence of differential antibody binding in the immune response to infectious disease
Authors: Chowdhury Robayet , Taguchi Alexander T. , Kelbauskas Laimonas , Stafford Phillip , Diehnelt Chris , Zhao Zhan-Gong , Williamson Phillip C. , Green Valerie , Woodbury Neal W.
Published: June 2023

Past studies have shown that incubation of human serum samples on high density peptide arrays followed by measurement of total antibody bound to each peptide sequence allows detection and discrimination of humoral immune responses to a variety of infectious diseases. This is true even though these arrays consist of peptides with near-random amino acid sequences that were not designed to mimic biological antigens. This “immunosignature” approach, is based on a statistical evaluation of the binding pattern for each sample but it ignores the information contained in the amino acid sequences that the antibodies are binding to. Here, similar array-based antibody profiles are instead used to train a neural network to model the sequence dependence of molecular recognition involved in the immune response of each sample. The binding profiles used resulted from incubating serum from 5 infectious disease cohorts (Hepatitis B and C, Dengue Fever, West Nile Virus and Chagas disease) and an uninfected cohort with 122,926 peptide sequences on an array. These sequences were selected quasi-randomly to represent an even but sparse sample of the entire possible combinatorial sequence space (~1012). This very sparse sampling of combinatorial sequence space was sufficient to capture a statistically accurate representation of the humoral immune response across the entire space. Processing array data using the neural network not only captures the disease-specific sequence-binding information but aggregates binding information with respect to sequence, removing sequence-independent noise and improving the accuracy of array-based classification of disease compared with the raw binding data. Because the neural network model is trained on all samples simultaneously, a highly condensed representation of the differential information between samples resides in the output layer of the model, and the column vectors from this layer can be used to represent each sample for classification or unsupervised clustering applications.
BioSeq-Diabolo: Biological sequence similarity analysis using Diabolo
Authors: Li Hongliang , Liu Bin
Published: June 2023

As the key for biological sequence structure and function prediction, disease diagnosis and treatment, biological sequence similarity analysis has attracted more and more attentions. However, the exiting computational methods failed to accurately analyse the biological sequence similarities because of the various data types (DNA, RNA, protein, disease, etc) and their low sequence similarities (remote homology). Therefore, new concepts and techniques are desired to solve this challenging problem. Biological sequences (DNA, RNA and protein sequences) can be considered as the sentences of “the book of life”, and their similarities can be considered as the biological language semantics (BLS). In this study, we are seeking the semantics analysis techniques derived from the natural language processing (NLP) to comprehensively and accurately analyse the biological sequence similarities. 27 semantics analysis methods derived from NLP were introduced to analyse biological sequence similarities, bringing new concepts and techniques to biological sequence similarity analysis. Experimental results show that these semantics analysis methods are able to facilitate the development of protein remote homology detection, circRNA-disease associations identification and protein function annotation, achieving better performance than the other state-of-the-art predictors in the related fields. Based on these semantics analysis methods, a platform called BioSeq-Diabolo has been constructed, which is named after a popular traditional sport in China. The users only need to input the embeddings of the biological sequence data. BioSeq-Diabolo will intelligently identify the task, and then accurately analyse the biological sequence similarities based on biological language semantics. BioSeq-Diabolo will integrate different biological sequence similarities in a supervised manner by using Learning to Rank (LTR), and the performance of the constructed methods will be evaluated and analysed so as to recommend the best methods for the users. The web server and stand-alone package of BioSeq-Diabolo can be accessed athttp://bliulab.net/BioSeq-Diabolo/server/.
Anti-angiogenic and anti-proliferative activity of ziziphus leaf extract as a novel potential therapeutic agent for reducing hepatic injury in experimental hamster schistosomiasis
Authors: Alghamdi Thamer , Salem Doaa A. , El-Refaei Mohamed F.
Published: June 2023

Background

Schistosomiasis is one of the most prevalent helminthic infections worldwide. Praziquantel (PZQ) resistance poses a possible danger to the disease’s ability to be controlled. Little is known about the role ofZiziphus spina-christileaf extract (ZLE) in the treatment of hepatic schistosomiasis. However, no study has explored ZLE’s anti-angiogenic and anti-proliferative activity as a possible mechanism for reducing hepatic injury in this context. Therefore, this study aimed to evaluate the therapeutic potential of ZLE as an anti-angiogenic, and anti-proliferative agent in hamsters infected withS.mansoni.

Methods

Fifty hamsters were used and divided into 5 groups (10 hamsters each); noninfected untreated (controls), noninfected treated with ZLE, infected untreated, infected treated with PZQ- and infected treated with ZLE. Anti-angiogenic and anti-fibrotic effects of the drugs were assessed pathologically through the immunohistochemical expression of VEGF, Ki-67, and TGF β1 in liver sections. Some oxidative stress parameters were measured in hepatic homogenates (NO, GSH, GST, and SOD), and serum liver enzymes were also assessed.

Results

A significant decrease in worm burden, granuloma size, granuloma area, and numbers in the ZLE- and PZQ-treated groups compared to the infected untreated group, and the decrease in granulomas number and tissue egg load was significantly lower in PZQ treated group compared to ZLE treated group (p<0.05). ZLE exhibited significant anti-angiogenic and anti-fibrotic effects on granulomas, illustrated by significantly lower expression of VEGF and TGF-β1 than infected untreated and PZQ-treated groups. ZLE exhibits antiproliferative activity evidenced by a significant reduction of positive Ki-67 hepatocytes percentage compared to the infected untreated group. Moreover, ZLE exhibits potent antioxidant effects evidenced by a significantly lowered NO and conservation of hepatic GSH, GST, and SOD in hepatic homogenates compared to infected untreated and PZQ-treated groups (p<0.05).

Conclusion

Our results point to ZLE as a promising hepatoprotective therapeutic tool in the treatment of schistosome hepatic fibrosis as it has anti-angiogenic, anti-proliferative, anti-fibrotic, and antioxidant effects in hamsters infected withS.mansoni, providing scientific support for its use in conventional medicine.
Association between altered cognition and Loa loa microfilaremia: First evidence from a cross-sectional study in a rural area of the Republic of Congo
Authors: Checkouri Thomas , Missamou François , Pion Sebastien D. S. , Bikita Paul , Hemilembolo Marlhand C. , Boussinesq Michel , Chesnais Cédric B. , Campillo Jérémy T.
Published: June 2023

Background

Individuals with high Loa loa microfilarial densities are at risk of developing severe encephalopathy after administration of antiparasitic drugs. Apart from this finding, loiasis is considered benign with no effect on brain function. However, recent epidemiological data suggest an increased mortality and morbidity in L. loa infected individuals, underscoring the importance of studies on the possible neurological morbidity associated with loiasis.

Methodology

Using MoCA tests and neurological ultrasounds, we conducted a cross-sectional study to assess cognitive alteration in a population living in a rural area endemic for loiasis in the Republic of Congo. Fifty individuals with high microfilarial densities (MFD) were matched on sex, age and residency with 50 individuals with low MFD and 50 amicrofilaremic subjects.

Analyses focused on individuals with MoCA scores indicating an altered cognition (i.e. < 23/30) and on the total MoCA score according to Loa loa MFD, sociodemographic characteristics and neurological ultrasound results.

Principal findings

MoCA scores were very low in the studied population (mean of 15.6/30). Individuals with more than 15,000 microfilariae per milliliter of blood (mean predicted score:14.0/30) are more than twenty times more likely to have an altered cognition, compared to individuals with no microfilaremia (mean predicted score: 16.3/30). Years of schooling were strongly associated with better MoCA results. Extracranial and intracranial atheroma were not associated with L. loa MFD.

Conclusion/significance

Loaisis microfilaremia is probably involved in cognitive impairment, especially when the MFD are high. These results highlight the urgent need to better understand loaisis-induced morbidity. Further studies investigating neurological morbidity of loiasis are needed.
Nodding syndrome, a case-control study in Mahenge, Tanzania: Onchocerca volvulus and not Mansonella perstans as a risk factor
Authors: Amaral Luís-Jorge , Bhwana Dan , Mhina Athanas D. , Mmbando Bruno P. , Colebunders Robert
Published: June 2023

Background

Nodding syndrome (NS) has been consistently associated with onchocerciasis. Nevertheless, a positive association between NS and aMansonella perstansinfection was found in South Sudan. We aimed to determine whether the latter parasite could be a risk factor for NS in Mahenge.

Methods

Cases of epilepsy were identified in villages affected by NS in Mahenge, Tanzania, and matched with controls without epilepsy of the same sex, age and village. We examined blood films of cases and controls to identifyM.perstansinfections. The participants were also asked for sociodemographic and epilepsy information, examined for palpable onchocercal nodules and onchocerciasis-related skin lesions and tested for anti-Onchocerca volvulusantibodies (Ov16 IgG4) by ELISA. Clinical characteristics of cases and controls,O.volvulusexposure status and relevant sociodemographic variables were assessed by a conditional logistic regression model for NS and epilepsy status matched for age, sex and village.

Results

A total of 113 epilepsy cases and 132 controls were enrolled, of which, respectively, 56 (49.6%) and 64 (48.5%) were men. The median age in cases and controls was 28.0 (IQR: 22.0–35.0) and 27.0 (IQR: 21.0–33.3) years. Of the persons with epilepsy, 43 (38.1%) met the probable NS criteria and 106 (93.8%) had onchocerciasis-associated epilepsy (OAE).M.perstansinfection was absent in all participants, while Ov16 seroprevalence was positively associated with probable NS (odds ratio (OR): 5.05, 95%CI: 1.79–14.27) and overall epilepsy (OR: 2.03, 95%CI: 1–07–3.86). Moreover, onchocerciasis-related skin manifestations were only found in the cases (n = 7, p = 0.0040), including persons with probable NS (n = 4, p = 0.0033). Residing longer in the village and having a family history of seizures were positively correlated with Ov16 status and made persons at higher odds for epilepsy, including probable NS.

Conclusion

In contrast toO.volvulus,M.perstansis most likely not endemic to Mahenge and, therefore, cannot be a co-factor for NS in the area. Hence, this filaria is unlikely to be the primary and sole causal factor in the development of NS. The main risk factor for NS remains onchocerciasis.
Identify novel elements of knowledge with word embedding
Authors: Yin Deyun , Wu Zhao , Yokota Kazuki , Matsumoto Kuniko , Shibayama Sotaro
Published: June 2023

As novelty is a core value in science, a reliable approach to measuring the novelty of scientific documents is critical. Previous novelty measures however had a few limitations. First, the majority of previous measures are based on recombinant novelty concept, attempting to identify a novel combination of knowledge elements, but insufficient effort has been made to identify a novel element itself (element novelty). Second, most previous measures are not validated, and it is unclear what aspect of newness is measured. Third, some of the previous measures can be computed only in certain scientific fields for technical constraints. This study thus aims to provide a validated and field-universal approach to computing element novelty. We drew on machine learning to develop a word embedding model, which allows us to extract semantic information from text data. Our validation analyses suggest that our word embedding model does convey semantic information. Based on the trained word embedding, we quantified the element novelty of a document by measuring its distance from the rest of the document universe. We then carried out a questionnaire survey to obtain self-reported novelty scores from 800 scientists. We found that our element novelty measure is significantly correlated with self-reported novelty in terms of discovering and identifying new phenomena, substances, molecules, etc. and that this correlation is observed across different scientific fields.
Total added sugar consumption is not significantly associated with risk for prediabetes among U.S. adults: National Health and Nutrition Examination Survey, 2013–2018
Authors: Sneed Nadia Markie , Azuero Andres , Moss Jacqueline , Goss Amy M. , Morrison Shannon A.
Published: June 2023

Prediabetes affects 38% of U.S. adults and is primarily linked to added sugars consumed from sugar-sweetened beverages. It is unclear if total dietary intake of added sugar also increases the risk for prediabetes. This study examined if total (g/day) and percent intakes of <10%, 10–15%, or >15% added sugar increase the odds for prediabetes in U.S. adults. A cross-sectional, secondary analysis using 2013–2018 NHANES data was conducted. This study included data from U.S. adults ≥ 20 years with normoglycemia (N = 2,154) and prediabetes (N = 3,152) with 1–2 days of dietary recall information. Prediabetes was defined as a hemoglobin A1c of 5.7%-6.4% or a fasting plasma glucose of 100–125 mg/dL. Survey-weighted logistic regression was used to estimate odds ratios of prediabetes based on usual intakes of added sugar (total and percent intakes) using the National Cancer Institute Method. Differences in prediabetes risk and total and percent intakes of added sugar were compared by race/ethnicity. The sample’s total energy intake from added sugar was 13.9%. Total (unadjusted: OR: 1.01, 95% CI: .99–1.00, p = .26; adjusted: OR: 1.00, 95% CI: .99–1.00, p = .91) and percent intakes of added sugar (unadjusted [<10%: (ref); 10–15%: OR: .93, 95% CI: .77–1.12, p = .44; >15%: OR: 1.03, 95% CI: .82–1.28, p = .82] and adjusted [<10%: (ref); 10–15%: OR: .82, 95% CI: .65–1.04, p = .09; >15%: OR: .96, 95% CI: .74–1.24, p = .73]) were not significantly associated with an increased odds of prediabetes. Prediabetes risk did not differ by race/ethnicity for total (unadjusted model [p = .65]; adjusted model [p = .51]) or percent (unadjusted model [p = .21]; adjusted model [p = .11]) added sugar intakes. In adults ≥20 years with normoglycemia and prediabetes, total added sugar consumption did not significantly increase one’s risk for prediabetes and risk estimates did not differ by race/ethnicity. Experimental studies should expand upon this work to confirm these findings.
Explaining machine-learning models for gamma-ray detection and identification
Authors: Bandstra Mark S. , Curtis Joseph C. , Ghawaly James M. , Jones A. Chandler , Joshi Tenzing H. Y.
Published: June 2023

As more complex predictive models are used for gamma-ray spectral analysis, methods are needed to probe and understand their predictions and behavior. Recent work has begun to bring the latest techniques from the field of Explainable Artificial Intelligence (XAI) into the applications of gamma-ray spectroscopy, including the introduction of gradient-based methods like saliency mapping and Gradient-weighted Class Activation Mapping (Grad-CAM), and black box methods like Local Interpretable Model-agnostic Explanations (LIME) and SHapley Additive exPlanations (SHAP). In addition, new sources of synthetic radiological data are becoming available, and these new data sets present opportunities to train models using more data than ever before. In this work, we use a neural network model trained on synthetic NaI(Tl) urban search data to compare some of these explanation methods and identify modifications that need to be applied to adapt the methods to gamma-ray spectral data. We find that the black box methods LIME and SHAP are especially accurate in their results, and recommend SHAP since it requires little hyperparameter tuning. We also propose and demonstrate a technique for generating counterfactual explanations using orthogonal projections of LIME and SHAP explanations.
Half-duplex and full-duplex interference mitigation in relays assisted heterogeneous network
Authors: Madani Fadoul Moubachir , Chow Chee-Onn
Published: June 2023

In a multicell environment, the half-duplex (HD) relaying is prone to inter-relay interference (IRI) and the full-duplex (FD) relaying is prone to relay residual-interference (RSI) and relay-to-destination interference (RDI) due to Next Generation Node B (gNB) traffic adaptation to different backhaul subframe configurations. IRI and RDI occur in the downlink when a relay is transmitting on its access link and interfering with the reception of a backhaul link of another victim relay. While the simultaneous transmission and reception of the FD relay creates the RSI. IRI, RDI, and RSI have detrimental effects on the system performance, leading to lower ergodic capacity and higher outage probability. Some previous contributions only briefly analysed the IRI, RSI, and RDI in a single cell scenario and some assumed that the backhaul and access subframes among the adjacent cells are perfectly aligned for different relays without counting for IRI, RSI and RDI. However, in practise the subframes are not perfectly aligned. In this paper, we eliminate the IRI, RSI, and RDI by using the hybrid zeroforcing and singular value decomposition (ZF-SVD) beamforming technique based on nullspace projection. Furthermore, joint power allocation (joint PA) for the relays and destinations is performed to optimize the capacity. The ergodic capacity and outage probability comparisons of the proposed scheme with comparable baseline schemes corroborate the effectiveness of the proposed scheme.
Overcrowded housing reduces COVID-19 mitigation measures and lowers emotional health among San Diego refugees from September to November of 2020
Authors: Hassani Ashkan , Omaleki Vinton , Erikat Jeanine , Frost Elizabeth , Streuli Samantha , Sahid Ramla , Yusufi Homayra , Fielding-Miller Rebecca
Published: June 2023

Refugee communities are vulnerable to housing insecurity, which drives numerous health disparity outcomes in a historically marginalized population. The COVID-19 pandemic has only worsened the ongoing affordable housing crisis in the United States while continuing to highlight disparities in health outcomes across populations. We conducted interviewer-administered surveys with refugee and asylum seekers in San Diego County at the height of the COVID-19 pandemic to understand the social effects and drivers of COVID-19 in one of the largest refugee communities in the United States. Staff from a community-based refugee advocacy and research organization administered the surveys from September—November 2020. 544 respondents participated in the survey, which captured the diversity of the San Diego refugee community including East African (38%), Middle Eastern (35%), Afghan (17%), and Southeast Asian (11%) participants. Nearly two-thirds of respondents (65%) reported living in overcrowded conditions (> 1 individual per room) and 30% in severely crowded conditions (> 1.5 individuals per room). For each additional person per room, self-reported poor emotional health increased. Conversely, family size was associated with a lower likelihood of reporting poor emotional health. Crowded housing was significantly associated with a lower probability of accessing a COVID-19 diagnostic test, with every additional reported person per room there was approximately an 11% increase in the probability of having never accessed a COVID-19 testing. Access to affordable housing had the largest effect size and was associated with fewer people per room. Overcrowding housing is a structural burden that reduces COVID-19 risk mitigation behaviors. Improved access to affordable housing units or receiving vouchers could reduce overcrowded housing in vulnerable refugee communities.