bluuebunny/crossref_metadata_2025 huggingface dataset:
Preparation, structural characterization and in vitro activity of ginger polysaccharide
Authors: Zhou Shiyang , Wang Xinqiao , Jiang Wenming , Tan Jun , Chen Guangying
Published: November 2023

A polysaccharide was extracted from the fresh ginger by water extraction and alcohol precipitation. A homogeneous polysaccharide was obtained by Sevage deproteinization, dialysis, DEAE-52 ion exchange chromatography and Sephadex G-100 gel column chromatography. The molecular weight of the ginger polysaccharide was determined by high performance gel permeation chromatography. The monosaccharide composition, scanning electron microscope and other physicochemical parameters of the ginger polysaccharide were further determined. The spectral properties of the ginger polysaccharide were investigated by ultraviolet and infrared spectroscopy. On this basis, methylation analysis, 1D and 2D NMR analysis were used to investigate its possible chemical structure. The results showed that the ginger polysaccharide group was divided into neutral polysaccharide components with high homogeneity, Mw = 35.52 kDa, Mn = 216.56 kDa and the sugar content was 93.5%. The ginger polysaccharide is mainly composed of Fuc, Ara, Rha, Gal, Glc, Xyl, Man, Gal-UA and Glc-UA, the amount of substance ratio was 1.01:1.96:9.54:14.82:64.20:3.84:2.07:1.41:1.16. To study the structure–activity relationship of ginger polysaccharide, acetylated ginger polysaccharide and phosphate ginger polysaccharide were prepared by chemical methods in this study. The results of antioxidant activity in vitro showed that the ginger polysaccharide and its derivatives had good biological activity in freeing ABTS + radical scavenging, freeing hydroxyl radical scavenging, freeing DPPH radical scavenging and reducing ability. Interestingly, the results showed that the ginger polysaccharide had a certain inhibitory effect on the growth of E. coli in vitro. In general, this study provides a certain experimental basis and reference for the further research on the activity of ginger polysaccharide and its derivatives.

Graphical Abstract
Water, sanitation and hygiene (WASH) practices and deworming improve nutritional status and anemia of unmarried adolescent girls in rural Bangladesh
Authors: Jolly Saira Parveen , Roy Chowdhury Tridib , Sarker Tanbi Tanaya , Afsana Kaosar
Published: November 2023

Background

In Bangladesh, undernutrition and anemia are more occurrent among adolescent girls. BRAC, the largest non-governmental organization (NGO), has been implementing a community-based nutrition education service package targeting adolescent girls for reducing their undernutrition and anemia.

Objective

We aimed to explore the underlying factors associated with nutritional status and anemia among adolescent girls under the BRAC nutrition program areas to improve their existing intervention package.

Methodology

We conducted a cross-sectional and comparative study in 2016, in 24 upazilas of Bogra, Barguna, Comilla, Dinajpur, Feni, Jessore, and Meherpur districts where the BRAC nutrition program was implemented while the remaining 27 upazilas of those districts were selected as comparison area. We followed a multistage cluster random sampling for selecting 1620 unmarried adolescent girls aged 10–19 years for interviewing in the intervention and comparison areas. Data were collected on socio-demographic information, dietary intake, morbidity, water, sanitation, and hygiene (WASH) practice, anthropometry, and serum hemoglobin (Hb) level by using a pre-structured questionnaire. The nutritional status of the adolescent girls was expressed as height-for-age Z (HAZ) and body mass index-for-age Z (BMIZ) score, while anemia referred to the serum Hb at the level of below 12 g/dl for adolescent girls. All statistical analyses were done in STATA version 17 (Chicago Inc.).

Findings

The prevalence of stunting (22.9% vs. 22.5%), thinness (12% vs. 14%), and anemia (34.5% vs. 37.3%) exhibited similarities between the intervention and comparison regions. Stunting and thinness were predictors for each other for this population group. Our findings indicated that adolescent girls who were not washing hands with soap after defecation were likely to be stunted [AOR 1.51 (95% CI 1.12–2.04)], and who did not utilize sanitary latrines had an increased likelihood of being thin [AOR 2.38 (95% CI 1.11–5.08)]. Conversely, those who did not watch television [AOR 1.69 (95% CI 1.12–2.56)] and did not have deworming tablets [AOR 1.33 (95% CI 1.07–1.64)] in the 6 months leading up to the interview had a 69% and 33% higher probability of being anemic, respectively.

Conclusion

For sustainable improvement in the undernutrition and anemia of adolescent girls, integration of WASH, consistent administration of deworming tablets and broadcasting awareness programs through television are urgent to scale up the nutrition intervention programs in similar settings like Bangladesh.
Added value of 3D ultrasound image-guided hepatic interventions by X matrix technology
Authors: Omar Hazem , Korayem Enas Mohammed , Khalil Ahmed Abdel Sattar , Abokoura Sameh
Published: November 2023

Background

Image-guided hepatic interventions are integral to the management of infective and neoplastic liver lesions. Over the past decades, 2D US was used for guidance of hepatic interventions; with the recent advances in US technology, 3D US was used to guide the hepatic interventions. This study aimed to illustrate the added value of 3D image-guided hepatic interventions by X matrix technology.

Methods

This prospective study was performed on 100 patients that were divided into two groups: group A which included 50 patients who were managed by using 2D US probe guidance, and group B which included 50 patients who were managed by using 3D X matrix US probe guidance. Thermal ablation was done for 70 patients; 40 radiofrequency ablation (RFA) (20 by the 2D probe and 20 by the 3D X matrix probe) and 30 microwave ablation (MWA) (15 by the 2D probe and 15 by the 3D X matrix probe). Chemical ablation (PEI) was done for 20 patients (ten by the 2D probe and ten by the 3D X matrix probe). Drainage of hepatic collections and biopsy from undiagnosed hepatic focal lesions were done for ten patients (five by the 2D probe and five by the 3D X matrix probe).

Results

The efficacy of US-guided hepatic interventions by 3D X matrix probe was higher than the 2D probe but not significantly higher, with a p value of 0.705, 0.5428 for RFA and MWA, respectively, 0.5312 for PEI, and 0.2918 for drainage of hepatic collections and biopsy. The complications related to the use of the 3D X matrix probe were significantly lower than the 2D probe with a p value of 0.003. The timing of the procedure was shorter by the usage of a 3D X matrix probe in comparison with the 2D probe with a p value of 0.08, 0.34 for RFA and PEI and significantly shorter for MWA and drainage of hepatic collection, biopsy with a p value of 0.02, 0.001, respectively.

Conclusions

3D US-guided hepatic interventions by X matrix probe have better efficacy, less complication, and shorter time of procedure than the 2D US-guided hepatic interventions.
Development of a subsea distributed acoustic sensing acquisition system
Authors: van Gestel Jean-Paul , Soulas Sebastien , Naldrett Garth
Published: November 2023

Over the past few decades, distributed acoustic sensing (DAS) data acquisition has seen great improvements from better interrogators, engineered fiber, and lessons learned from subsea installation and acquisition. This has given us confidence that DAS cables can be installed in wells with subsea trees to be used as receivers for vertical seismic profile (VSP) seismic imaging. VSP imaging for deepwater fields has been demonstrated to provide better illumination and higher-frequency seismic data. Permanent DAS cable installation can be used to acquire highly repeatable time-lapse (4D) data. DAS cables have been installed in a number of subsea wells on two deepwater oil fields with the intention of covering the crest of these fields with high-frequency seismic data. A system has been developed to allow for DAS acquisition on these offshore subsea wells with long-distance tie backs using permanently installed interrogators on the floating platforms and engineered fiber in the wells. On each of these fields, a DAS cable has now been installed, and subsequently, a zero offset (ZO) DAS VSP has been acquired for verification and commissioning. These ZO DAS VSP acquisitions indicate high-fidelity installations resulting in DAS VSP data with excellent data quality. These first subsea DAS acquisitions indicate great promise, and further installations and acquisitions are planned with the ultimate goal of providing high-frequency seismic images over the crest of these fields to reduce the uncertainty in decisions around reservoir management and future infill drilling.
“I Want to Be Involved in Constructing the World”: In Discussion with Malala Andrialavidrazana
Authors: Diabate Naminata
Published: November 2023

On Sunday, February 26, 2023, Naminata Diabate met over Zoom with visual artist Malala Andrialavidrazana, whose most recent works have been exhibited at the Boghossian Foundation in Brussels and the Centre Pompidou in Paris. Based on extensive in situ as well as bibliographic and archival research, Andrialavidrazana's visual compositions offer the possibility of alternative forms of storytelling and world-making. In this interview, the artist, whose interest spans centuries and all corners of the globe, shared how the political and racial landscape of her country of origin, Madagascar, and her family background shape her artistic expression and her place in the world.
Association between nitric oxide and cancer and stroke risk: A meta-analysis
Authors: Tualeka Abdul Rohim , Jalaludin Juliana , Gasana Janvier , Sopian Nor Ashikin , Chao How Ran , Yusmaidie Mohd , Perumal Velu , Zurimi Suardi , Rahmawati Pudji , Ahsan Ahsan , Novianti Salsabila
Published: November 2023

Background: Numerous case-control studies have been carried out to test the mechanism by which nitric oxide, specifically the polymorphism 894G>T in the eNOS gene, or endothelial nitric oxide synthase, raises the possibility of stroke and cancer. 

Methods: The aim of this meta-analysis was to describe the correlation between cancer and stroke risk with nitric oxide, by implementing a comprehensive search in various digital databases, including Science Direct, PubMed, and Google Scholar, in the period 2012-2023 to observe the published results of all related studies. 

Results: The meta-analysis included a total of fifteen case-control studies. These studies involved 3,019 cases and 3,333 controls in total. This study found that the GG versus GT+TT genotype of eNOS 894G>T polymorphism was significantly positively correlated with cancer risk. Additionally, the significance of this association was further attributed to the specific type of polymorphism involved, as well as the risk of stroke in the T versus G model, followed by TT versus GG+GT.

Conclusions: The results of the eNOS 894G>T polymorphisms have been correlated with cancer, and in particular, the GT+TT  versus GG model yielded an odds ratio (OR of 1.96, a 95% CI of 1.22 to 3.15, and a p-value of 0.0005. Moreover, the mentioned polymorphisms were found to be associated with stroke risk in the T versus G model, which had an OR of 1.20; 95% CI of 1.01 to 1.43 with a p-value of 0.04; and TT versus GG+GT with an OR of 0.09; 95% CI of 0.03 to 0.30 with a p-value of 0.0001.
Plackett-Burman design in the biosynthesis of silver nanoparticles with Mutisia acuminatta (Chinchircoma) and preliminary evaluation of its antibacterial activity
Authors: Laime-Oviedo Luis A. , Arenas-Chávez Carlos A. , Yáñez Jaime A. , Vera-Gonzáles Corina A.
Published: November 2023

Background: The aim of this study was to synthesize silver nanoparticles (AgNPs) using the methanolic fraction of Mutisia acuminatta leaves using Plackett-Burman design to optimize process parameters and to evaluate its antibacterial effect.

Methods: For the separation of Mutisia acuminatta phytoconstituents, chromatographic techniques were used. For characterization and identification, UV - VIS spectrophotometry, FTIR spectrophotometry, Dynamic Light Scattering (DLS) and transmission electron microscopy (TEM) were used. The Plackett-Burman design used polynomial regression statistical analysis to determine the most influential variables.

Results: UV-VIS spectroscopy reported an absorbance concerning surface plasmon resonance between 410–420 nm wavelength for the AgNPs. FTIR spectrophotometry reported characteristic peaks in the biosynthesized AgNPs , observing the disappearance of spectral peaks between 1000–1500 cm-1. By UHPLC-MS, caffeic acid derivatives, coumarins, flavonoids, lignans, disaccharide and a complex formed between silver and the solvent (AgCH3CN+) were identified. Using DLS, the AgNPs presented an average hydrodynamic size of 45.91 nm. TEM determined the spherical shape of the AgNPs, presenting diameters in the range of 30 to 60 nm. The biosynthesized AgNPs showed higher antibacterial activity against Escherichia coli and Staphylococcus aureus than the total extract, the methanolic fraction and pure methanol. The polynomial model in the biosynthesis was validated with an adequate fitting representing the experimental data of the process. The most significant variables for the model obtained were the reaction pH (X2) and the concentration of the precursor salt AgNO3 (X6).

Conclusions: The synthesized AgNPs offer a viable option for further development due to the presence of bioactive compounds, adequate characterization and antibacterial activity.
Ranking of the Leading Russian Evaluation Organizations and Groups: Results of 2022
Authors: Khanferyan V.
Published: November 2023

The annual, nineteenth edition of the rankings of leading valuation companies compiled by the RAEX agency ("RAEX-Analytics") demonstrates stagnation in the market of valuation services.
Personnel Management Audit in Housing and Communal Services Company
Authors: Zykova T. , Kupriyanova T.
Published: November 2023

The article explores approaches to the concept of «HR audit» and formulates the definition of HR audit from the point of view of the process approach. The paper presents a description of the audit process of personnel management, its elements and sequence, proposes a strategy and plan for auditing personnel management of the managing organization, defines control procedures for auditing personnel management of the managing organization, formulates requirements for the structure and content of the report based on the results of the personnel management audit.
Body biographies: a study of apprenticeship and embodied experience among tattoo artists in Mexico
Authors: González Varela Sergio
Published: November 2023

Based on the author’s long-term fieldwork experience in Mexico, this article describes the apprenticeship experience of tattoo artists. It deals with the learning process of a craft, how artists develop skills and techniques, and how they share their knowledge with others. The text argues that the solidarity that the tattoo community creates passes not only through the relationship between artists and clients but also through the exchange and reciprocity between professionals through the mutual inking of their bodies, in what the author calls body biographies. The article also depicts the importance of social media in promoting an artist’s work and how a person becomes an expert or a professional. Finally, it analyzes the growing popularity of tattoos and the saturated market it creates, where artists compete for clients, prestige, and money.
When epidemics become narrative, women get bogged down in scripts?
Authors: Skórzyńska Izabela
Published: November 2023

In the article, I follow the fate of women - heroines of the pandemic non-fiction literature in Poland, in order to verify the thesis that when women's experiences, such as pandemics or epidemics, become narratives, they themselves get stuck in women's narrative scripts and their variants characteristic of a specific culture. Treating storytelling, in the vein of anthropologists, as a primarily  cultural practice, I wonder whether and how the attribution and/or adoption of stories about their own experiences by the heroines of the pandemic and epidemic, enables them  to transgress the boundaries of scripts harmful to them, not invalidating their agency, but loudly manifesting their own point of view, different from the one established in culture.
Insulin-like growth factor-1 short-period therapy improves Non-Alcoholic Fatty Liver Disease (NAFLD) in obese mice
Authors: Daniela C. Andrade  , Filipe Jorge Nascimento  , Genilza P. de Oliveira  , Thiago Freire  , Simone N. de Carvalho  , Ana Carolina Stumbo  , Laís Carvalho  , Alessandra A. Thole  , Erika Cortez
Published: November 2023

This study seeks to evaluate Insulin-like Growth Factor 1 (IGF-1) short-period therapy in Non-Alcoholic Fatty Liver Disease (NAFLD) as it relates to western diet-induced obesity. For this purpose, 21-day-old male Swiss mice were divided into a control group (CG, N=8), which was fed a standard diet, and an obese group (GO, N=16), which was fed a western diet, rich in saturated fat and simple carbohydrates, for 12 weeks. In the 11th week, part of the animals in the obese group (N=8) received a daily subcutaneous injection of recombinant human IGF-1 (100µg/kg/day) during seven consecutive days (GO+IGF-1). Biometric and metabolic parameters, intraperitoneal glucose tolerance test (IGTT), quantitative analysis of liver steatosis, quantitative analysis of collagen in liver and expression of immunoperoxidase of alpha-smooth muscle actin (a-SMA) were analyzed. Our data demonstrated that IGF-1 short-term treatment was able to improve obesity-related biometric and metabolic parameters. In addition, it promoted the recovery of liver parenchyma, thereby reducing steatosis and fibrosis, thus demonstrating an important hepatoprotective action.
Letter to the editor: The challenge of carbapenem resistance
Authors: Silvia T. Castro  , José Augusto A. Pereira  , Eduardo A. R. de Castro
Published: November 2023

The global resistance of microorganisms to antimicrobials is one of the biggest public health challenges in recent decades however, among Gram-negative microorganisms, this problem has become very relevant, resulting in a shortage of medicines for the treatment of infections caused by these multi-resistant bacterial agents. Knowing the evolution of this resistance, among microorganisms in the hospital environment, is essential for: the projection of resistance in the coming decades, the rational use of antimicrobials and the adoption of measures to minimize their impact in this scenario. The most modern antimicrobial agents, which act on multi-resistant bacteria, are expensive, making their availability and use even more difficult, especially in the public health network in developing countries. However, new drugs for treating multidrug-resistant infections, due to their high cost, are often not available.
Apontamentos Históricos do Conceito de Esquizofrenia em Escritos de Vigotski (1930-1934)
Authors: Torres Luan , Santos Oswaldo , Ferreira Raíssa , Oliveira Adélia
Published: November 2023

Este artigo descreve os indícios históricos de proposições teóricas vigotskianas sobre o conceito de esquizofrenia, as quais são, comumente, apresentadas por meio de estudos de seus sintomas com intuito primordial de teorizar sobre a estrutura e funcionamento da consciência em seu desenvolvimento normal. A coleta de dados da descrição foi realizada, em 2020, em diversas plataformas de publicação de artigos e de livros em fonte secundária, com os descritores "esquizofrenia" e "Vigotski", bem como de recentes escritos divulgados e traduzidos do autor, em fontes primárias. Os resultados indicam que os sintomas da esquizofrenia são decorrentes da desintegração do pensamento por conceitos que, por conseguinte, interferem de maneira deletéria na afetividade e consciência da realidade; que, na adolescência, o pensamento conceitual, em sua estrutura, apresenta o anterior superado; que o desenvolvimento é a chave para entender os processos patológicos, os processos de dissociação das sínteses, das unidades superiores. Conclui-se que as contribuições vigotskianas sobre a esquizofrenia apontam para a interdependência da formação e da deformação das funções psicológicas superiores, especialmente na adolescência.
Optimal data acquisition in tomography
Authors: Javidan Mahshad , Esfandi Hadi , Anderson Rozalyn , Pashaie Ramin
Published: November 2023

In tomography, three-dimensional images of a medium are reconstructed from a set of two-dimensional projections. Each projection is the result of a measurement made by the scanner via radiating some form of energy and collecting the scattered field after interacting with the medium. The information content of these measurements is not equal, and one projection can be more informative than others. By choosing the most informative measurement at every step of scanning, an optimal tomography system can maximize the speed of data acquisition and temporal resolution of acquired images, reducing the operation cost and exposure to possible harmful radiations. The aim of this paper is to introduce mathematical algorithms that can be used to design measurements with optimal information content when imaging static or dynamically evolving objects.
Forward and backward propagation guided-mode waves of electric dipole resonances in an h-BN metasurface
Authors: Zhou Sheng , Jin Gao , Zhao Yue , Zhang Qiang , Fu Shu Fang , Wang Xiang Guang , Wang Xuan , Wang Xuan Zhang
Published: November 2023

The generation of a backward propagation (BP) and forward propagation (FP) guided mode in a double ridge h-BN metasurface (DRM) is investigated. h-BN is a hyperbolic metamaterial with two Reststrahlen frequency bands (RBs). The incident wave can excite guided modes in DRM, where the Poynting vector parallel component of the FP mode is identical and the BP mode is opposite to that of the incident wave. Based on the optimized structure, the frequency range of the BP mode for TE waves was found near the type II hyperbolic band (HB II), while for TM waves, it was found in the gap between the range of HB I and HB II in h-BN. To comprehensively understand the physics underlying BP and FP modes, we present the electric and magnetic field intensities in DRM, the electric field profile of beam steering, and the radiated powers of multipole resonances. The electric dipole (ED) moment contributes most significantly to the FP and BP modes, with its power being much greater than that of other multipolar moment modes. A proportion of BP mode power and incident power decreases with increasing incident angle of TE waves. There are two peaks of the proportion with TM waves. The maximum proportion is near 75% ofTE waves and 16% ofTM waves. The DRM has shown promising potential in the field of sensors based on BP mode, with a sensitivity of 3.9675 µm/RIU of TE waves and 5.1479 µm/RIU of TM waves. These findings suggest that DRMs hold significant promise for the development of optical metasurfaces, optical switches, and high-performance sensors.
Giant and tunable 2D-chiroptical response in few-layer borophene metasurfaces
Authors: Cheng Min
Published: November 2023

The 2D-chiroptical response in few-layer borophene metasurfaces (FBMs) is studied theoretically. By stacking borophene metasurfaces with the same physical parameters near the topological transition for the borophene metasurface, it is found that there exists strong 2D chirality, which can be controlled by the incident angle and the twist angle between the metasurfaces. When the borophene metasurfaces with different electron densities are stacked, the strong circular conversion dichroism (CCD) is found near the corresponding topological transition frequency for each borophene metasurface, resulting in the formation of the multiband CCD spectra. It is demonstrated that in the FBM there exists an ultrahigh sensitivity of the CCD to the substrate refractive index.
Advanced thin films of indium-tin oxide doping with photosensitive polymer via embossing process
Authors: Oh Jin Young , Kim Dong Hyun , Yang Da-Bin , Choi Bo-Kyeong , Lee Dong Wook , Park Hong-Gyu , Seo Dae-Shik
Published: November 2023

We propose a sol-gel thin film formation process involving nanoimprint lithography. First, indium tin oxide was dissolved in 2-methoxyethanol at a ratio of 5:5 and the mixture were mixed with 10 wt% of a UV-curable. Subsequently, a polydimethylsiloxane sheet prepared by covering a silicon wafer with a polydimethylsiloxane mold was attached to a InSnO thin film to duplicate the nanostructure through UV irradiation exposure. The replicated nanostructured thin films formed about morphological and chemical composition changes on the surface, we progressed to x-ray photoelectron spectroscopy and atomic force microscopy analysis. Furthermore, atomic force microscopy image analysis showed superior patterned grooves for a UV exposure time of 3 min. A suitability test involving the measurement of the transmittance was performed for examining the suitability of the thin film for use in display devices.
Simultaneous measurement of orthogonal terahertz fields via an emission multiplexing scheme
Authors: Ou Huiliang , Stantchev Rayko Ivanov , Chen Xuequan , Blu Thierry , Semtsiv Mykhaylo , Masselink William Ted , Serrano Arturo Hernandez , Costa Goncalo , Young Jacob , Chopra Nishtha , Lloyd-Hughes James , MacPherson Emma
Published: November 2023

We propose a polarization sensitive terahertz time-domain spectrometer that can record orthogonally polarized terahertz fields simultaneously, using fibre-coupled photoconductive antennas and a scheme that modulated the emitter’s polarization. The s and p channels of the multi-pixel terahertz emitter were modulated at different frequencies, thereby allowing orthogonal waveforms to be demultiplexed from the recorded signal in post-processing. The performance of the multi-pixel emitter used in this multiplexing scheme was comparable to that of a commercial single-polarization H-dipole antenna. The approach allowed two orthogonally polarized terahertz pulses to be recorded with good signal to noise (>1000:1) within half a second. We verified the capability of the spectrometer by characterizing a birefringent crystal and by imaging a polarization-sensitive metamaterial. This work has significant potential to improve the speed of terahertz polarization sensitive applications, such as ellipsometry and imaging.
Time alignment quantum illumination based on single real-time coincidence counting
Authors: Gao Wen-long , Xu Lu-ping , Zhang Hua
Published: November 2023

We propose and demonstrate an improved quantum illumination protocol based on the time correlation of twin photons, for the high signal-to-noise ratio (SNR) of target detection and signal reconstruction in the strong noise environment. The Hong-Ou-Mandel (HOM) interferometer is applied after the spontaneous parametric down-conversion (SPDC) process to construct a probing twin-beam in which the photon times are precisely aligned between the beams. At the radar receiver, we put forward a single real-time coincidence counting (SRCC) method on a series of time slices to reconstruct the probe signals of pulse radar and calculate the SNR advantages against the conventional pulse radar, as well as the quantum illumination (QI) protocol. Our main achievements in this research are the realization of real-time detection of quantum information while acquiring a higher SNR than QI and classical illumination (CI) protocols, as well as its demonstration of strong robustness to noise and losses, which also proposes what we believe to be a novel way for quantum target detection.
Spherical wave illumination scanning digital holographic profilometry
Authors: Wen Kai , Idicula Moncy Sajeev , Józwik Michał , Choo Hyon-Gon , Gao Peng , Kozacki Tomasz
Published: November 2023

In this work, we proposed what we believe to be a novel scanning solution for the assessment of high-NA samples, referred to as spherical-wave illumination scanning digital holographic profilometry (SWS-DHP). This approach introduces a 2F optimization methodology, based on the measurement of the focal length of the object to determine the spherical component of the scanning. Furthermore, re-optimization of 2F, whether it needs to be operated depends on the measured object's NA to inspect more information. Meanwhile, utilizing phase space analysis shows SWS superiority in information transfer for high-NA samples compared to plane-wave illumination scanning. In addition, this method introduces a shape reconstruction algorithm with volumetric aberration compensation based on the propagation of the aberrated object and illumination waves to obtain high-quality measurements. Finally, the imaging merits of SWS-DHP were proved through simulations and were experimentally verified for the object of NA up to 0.87.
Hybrid photonic integrated circuits for neuromorphic computing [Invited]
Authors: Xu Rongyang , Taheriniya Shabnam , Ovvyan Anna P. , Bankwitz Julian Rasmus , McRae Liam , Jung Erik , Brückerhoff-Plückelmann Frank , Bente Ivonne , Lenzini Francesco , Bhaskaran Harish , Pernice Wolfram H. P.
Published: November 2023

The burgeoning of artificial intelligence has brought great convenience to people’s lives as large-scale computational models have emerged. Artificial intelligence-related applications, such as autonomous driving, medical diagnosis, and speech recognition, have experienced remarkable progress in recent years; however, such systems require vast amounts of data for accurate inference and reliable performance, presenting challenges in both speed and power consumption. Neuromorphic computing based on photonic integrated circuits (PICs) is currently a subject of interest to achieve high-speed, energy-efficient, and low-latency data processing to alleviate some of these challenges. Herein, we present an overview of the current photonic platforms available, the materials which have the potential to be integrated with PICs to achieve further performance, and recent progress in hybrid devices for neuromorphic computing.
Additional Insights Into the Role of Osteocalcin in Osteoblast Differentiation and in the Early Steps of Developing Alveolar Process of Rat Molars
Authors: da Silva Sasso Gisela Rodrigues , Florencio-Silva Rinaldo , de Pizzol-Júnior José Paulo , Gil Cristiane Damas , Simões Manuel de Jesus , Sasso-Cerri Estela , Cerri Paulo Sérgio
Published: November 2023

This study investigated whether osteocalcin (OCN) is present in osteoblast precursors and its relationship with initial phases of alveolar process formation. Samples of maxillae of 16-, 18-, and 20-day-old rat embryos (E16, E18, and E20, respectively), and 05-, 10-, and 15-day-old postnatal rats (P05, P10, and P15, respectively) were fixed and embedded in paraffin or araldite. Immunohistochemistry for osterix (Osx), alkaline phosphatase (ALP), and OCN detection was performed and the number of immunolabelled cells was computed. Non-decalcified sections were subjected to the von Kossa method combined with immunohistochemistry for Osx or OCN detection. For OCN immunolocalization, samples were fixed in 0.5% glutaraldehyde/2% formaldehyde and embedded in LR White resin. The highest number of ALP- and OCN-immunolabelled cells was observed in dental follicle of E16 specimens, mainly in basal portions of dental alveolus. In corresponding regions, osteoblasts in differentiation adjacent to von Kossa-positive bone matrix exhibited Osx and OCN immunoreactivity. Ultrastructural analysis revealed OCN immunoreactive particles inside osteoblast in differentiation, and in bone matrix associated with collagen fibrils and within matrix vesicles, at early stages of alveolar process formation. Our results indicate that OCN plays a role in osteoblast differentiation and may regulate calcium/phosphate precipitation during early mineralization of the alveolar process:
External mechanical loading overrules cell-cell mechanical communication in sprouting angiogenesis during early bone regeneration
Authors: Dazzi Chiara , Mehl Julia , Benamar Mounir , Gerhardt Holger , Knaus Petra , Duda Georg N. , Checa Sara
Published: November 2023

Sprouting angiogenesis plays a key role during bone regeneration. For example, insufficient early revascularization of the injured site can lead to delayed or non-healing. During sprouting, endothelial cells are known to be mechano-sensitive and respond to local mechanical stimuli. Endothelial cells interact and communicate mechanically with their surroundings, such as outer-vascular stromal cells, through cell-induced traction forces. In addition, external physiological loads act at the healing site, resulting in tissue deformations and impacting cellular arrangements. How these two distinct mechanical cues (cell-induced and external) impact angiogenesis and sprout patterning in early bone healing remains however largely unknown. Therefore, the aim of this study was to investigate the relative role of externally applied and cell-induced mechanical signals in driving sprout patterning at the onset of bone healing. To investigate cellular self-organisation in early bone healing, an in silico model accounting for the mechano-regulation of sprouting angiogenesis and stromal cell organization was developed. Computer model predictions were compared to in vivo experiments of a mouse osteotomy model stabilized with a rigid or a semirigid fixation system. We found that the magnitude and orientation of principal strains within the healing region can explain experimentally observed sprout patterning, under both fixation conditions. Furthermore, upon simulating the selective inhibition of either cell-induced or externally applied mechanical cues, external mechanical signals appear to overrule the mechanical communication acting on a cell-cell interaction level. Such findings illustrate the relevance of external mechanical signals over the local cell-mediated mechanical cues and could be used in the design of fracture treatment strategies for bone regeneration.
Inferring microbial interactions with their environment from genomic and metagenomic data
Authors: Brunner James D. , Gallegos-Graves Laverne A. , Kroeger Marie E.
Published: November 2023

Microbial communities assemble through a complex set of interactions between microbes and their environment, and the resulting metabolic impact on the host ecosystem can be profound. Microbial activity is known to impact human health, plant growth, water quality, and soil carbon storage which has lead to the development of many approaches and products meant to manipulate the microbiome. In order to understand, predict, and improve microbial community engineering, genome-scale modeling techniques have been developed to translate genomic data into inferred microbial dynamics. However, these techniques rely heavily on simulation to draw conclusions which may vary with unknown parameters or initial conditions, rather than more robust qualitative analysis. To better understand microbial community dynamics using genome-scale modeling, we provide a tool to investigate the network of interactions between microbes and environmental metabolites over time.

Using our previously developed algorithm for simulating microbial communities from genome-scale metabolic models (GSMs), we infer the set of microbe-metabolite interactions within a microbial community in a particular environment. Because these interactions depend on the available environmental metabolites, we refer to the networks that we infer as metabolically contextualized, and so name our tool MetConSIN: Metabolically Contextualized Species Interaction Networks.
Checkpoint phosphorylation sites on budding yeast Rif1 protect nascent DNA from degradation by Sgs1-Dna2
Authors: Gali Vamsi Krishna , Monerawela Chandre , Laksir Yassine , Hiraga Shin-ichiro , Donaldson Anne D.
Published: November 2023

In budding yeast the Rif1 protein is important for protecting nascent DNA at blocked replication forks, but the mechanism has been unclear. Here we show that budding yeast Rif1 must interact with Protein Phosphatase 1 to protect nascent DNA. In the absence of Rif1, removal of either Dna2 or Sgs1 prevents nascent DNA degradation, implying that Rif1 protects nascent DNA by targeting Protein Phosphatase 1 to oppose degradation by the Sgs1-Dna2 nuclease-helicase complex. This functional role for Rif1 is conserved from yeast to human cells. Yeast Rif1 was previously identified as a target of phosphorylation by the Tel1/Mec1 checkpoint kinases, but the importance of this phosphorylation has been unclear. We find that nascent DNA protection depends on a cluster of Tel1/Mec1 consensus phosphorylation sites in the Rif1 protein sequence, indicating that the intra-S phase checkpoint acts to protect nascent DNA through Rif1 phosphorylation. Our observations uncover the pathway by which budding yeast Rif1 stabilises newly synthesised DNA, highlighting the crucial role Rif1 plays in maintaining genome stability from lower eukaryotes to humans.
Genome mining yields putative disease-associated ROMK variants with distinct defects
Authors: Nguyen Nga H. , Sarangi Srikant , McChesney Erin M. , Sheng Shaohu , Durrant Jacob D. , Porter Aidan W. , Kleyman Thomas R. , Pitluk Zachary W. , Brodsky Jeffrey L.
Published: November 2023

Bartter syndrome is a group of rare genetic disorders that compromise kidney function by impairing electrolyte reabsorption. Left untreated, the resulting hyponatremia, hypokalemia, and dehydration can be fatal, and there is currently no cure. Bartter syndrome type II specifically arises from mutations in KCNJ1, which encodes the renal outer medullary potassium channel, ROMK. Over 40 Bartter syndrome-associated mutations in KCNJ1 have been identified, yet their molecular defects are mostly uncharacterized. Nevertheless, a subset of disease-linked mutations compromise ROMK folding in the endoplasmic reticulum (ER), which in turn results in premature degradation via the ER associated degradation (ERAD) pathway. To identify uncharacterized human variants that might similarly lead to premature degradation and thus disease, we mined three genomic databases. First, phenotypic data in the UK Biobank were analyzed using a recently developed computational platform to identify individuals carrying KCNJ1 variants with clinical features consistent with Bartter syndrome type II. In parallel, we examined genomic data in both the NIH TOPMed and ClinVar databases with the aid of Rhapsody, a verified computational algorithm that predicts mutation pathogenicity and disease severity. Subsequent phenotypic studies using a yeast screen to assess ROMK function—and analyses of ROMK biogenesis in yeast and human cells—identified four previously uncharacterized mutations. Among these, one mutation uncovered from the two parallel approaches (G228E) destabilized ROMK and targeted it for ERAD, resulting in reduced cell surface expression. Another mutation (T300R) was ERAD-resistant, but defects in channel activity were apparent based on two-electrode voltage clamp measurements in X. laevis oocytes. Together, our results outline a new computational and experimental pipeline that can be applied to identify disease-associated alleles linked to a range of other potassium channels, and further our understanding of the ROMK structure-function relationship that may aid future therapeutic strategies to advance precision medicine.
Fungal mycetoma and pregnancy: An association with costly and difficult management, about a case
Authors: Ndour Niare , Ndiaye Mame Tené , Diop Assane , Ly Ramatoulaye , Ndiaye Coumba , Sarr Mamadou , Diouf Astou , Diagne Fatou , Ly Fatimata
Published: November 2023

Mycetomas are endemic diseases in tropical and sub-tropical countries of Africa, Asia and America, mainly affecting rural populations living below the poverty line. We report a particular case of a mycetoma associated with pregnancy whose evolution was good, but at the cost of significant financial expenses. This was a 39-year-old woman who developed a fungal mycetoma due to Madurella mycetomatis from the ingunocrural region. The patient had to develop several previous pregnancies on this site of mycetoma, the outcome of which was favorable. The last pregnancy was accompanied by an aggravation of the mycetoma in the form of polyfistulized inflammatory swelling of the right inguino-crural region emitting black grains. Magnetic Resonance Imaging (MRI) of the region showed invasion of the adductor muscles at the level of the root of the thigh on its antero-internal side with no sign of pelvic extension or underlying bone lesion. The patient was treated by surgery associated with antifungal treatment. The evolution was favorable for pregnancy and mycetoma.
Wide reference databases for typing Trypanosoma cruzi based on amplicon sequencing of the minicircle hypervariable region
Authors: Rusman Fanny , Díaz Anahí G. , Ponce Tatiana , Floridia-Yapur Noelia , Barnabé Christian , Diosque Patricio , Tomasini Nicolás
Published: November 2023

Background

Trypanosoma cruzi, the etiological agent of Chagas Disease, exhibits remarkable genetic diversity and is classified into different Discrete Typing Units (DTUs). Strain typing techniques are crucial for studying T. cruzi, because their DTUs have significant biological differences from one another. However, there is currently no methodological strategy for the direct typing of biological materials that has sufficient sensitivity, specificity, and reproducibility. The high diversity and copy number of the minicircle hypervariable regions (mHVRs) makes it a viable target for typing.

Methodology/Principal findings

Approximately 24 million reads obtained by amplicon sequencing of the mHVR were analyzed for 62 strains belonging to the six main T. cruzi DTUs. To build reference databases of mHVR diversity for each DTU and to evaluate this target as a typing tool. Strains of the same DTU shared more mHVR clusters than strains of different DTUs, and clustered together. Different identity thresholds were used to build the reference sets of the mHVR sequences (85% and 95%, respectively). The 95% set had a higher specificity and was more suited for detecting co-infections, whereas the 85% set was excellent for identifying the primary DTU of a sample. The workflow’s capacity for typing samples obtained from cultures, a set of whole-genome data, under various simulated PCR settings, in the presence of co-infecting lineages and for blood samples was also assessed.

Conclusions/Significance

We present reference databases of mHVR sequences and an optimized typing workflow for T. cruzi including a simple online tool for deep amplicon sequencing analysis (https://ntomasini.github.io/cruzityping/). The results show that the workflow displays an equivalent resolution to that of the other typing methods. Owing to its specificity, sensitivity, relatively low cost, and simplicity, the proposed workflow could be an alternative for screening different types of samples.
Implementation and empirical evaluation of a quantum machine learning pipeline for local classification
Authors: Zardini Enrico , Blanzieri Enrico , Pastorello Davide
Published: November 2023

In the current era, quantum resources are extremely limited, and this makes difficult the usage of quantum machine learning (QML) models. Concerning the supervised tasks, a viable approach is the introduction of a quantum locality technique, which allows the models to focus only on the neighborhood of the considered element. A well-known locality technique is thek-nearest neighbors (k-NN) algorithm, of which several quantum variants have been proposed; nevertheless, they have not been employed yet as a preliminary step of other QML models. Instead, for the classical counterpart, a performance enhancement with respect to the base models has already been proven. In this paper, we propose and evaluate the idea of exploiting a quantum locality technique to reduce the size and improve the performance of QML models. In detail, we provide (i) an implementation in Python of a QML pipeline for local classification and (ii) its extensive empirical evaluation. Regarding the quantum pipeline, it has been developed using Qiskit, and it consists of a quantumk-NN and a quantum binary classifier, both already available in the literature. The results have shown the quantum pipeline’s equivalence (in terms of accuracy) to its classical counterpart in the ideal case, the validity of locality’s application to the QML realm, but also the strong sensitivity of the chosen quantumk-NN to probability fluctuations and the better performance of classical baseline methods like the random forest.
Hazard potential of Swiss Ixodes ricinus ticks: Virome composition and presence of selected bacterial and protozoan pathogens
Authors: Stegmüller Stefanie , Qi Weihong , Torgerson Paul R. , Fraefel Cornel , Kubacki Jakub
Published: November 2023

Ticks play an important role in transmitting many different emerging zoonotic pathogens that pose a significant threat to human and animal health. In Switzerland and abroad, the number of tick-borne diseases, in particular tick-borne encephalitis (TBE), has been increasing over the last few years. Thus, it remains essential to investigate the pathogen spectrum of ticks to rapidly detect emerging pathogens and initiate the necessary measures. To assess the risk of tick-borne diseases in different regions of Switzerland, we collected a total of 10’286 ticks from rural and urban areas in ten cantons in 2021 and 2022. Ticks were pooled according to species, developmental stage, gender, and collection site, and analyzed using next generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR). The metagenomic analysis revealed for the first time the presence of Alongshan virus (ALSV) in Swiss ticks. Interestingly, the pool-prevalence of ALSV was higher than that of tick-borne encephalitis virus (TBEV). Furthermore, several TBEV foci have been identified and pool prevalence of selected non-viral pathogens determined.
Combining formal methods and Bayesian approach for inferring discrete-state stochastic models from steady-state data
Authors: Klein Julia , Phung Huy , Hajnal Matej , Šafránek David , Petrov Tatjana
Published: November 2023

Stochastic population models are widely used to model phenomena in different areas such as cyber-physical systems, chemical kinetics, collective animal behaviour, and beyond. Quantitative analysis of stochastic population models easily becomes challenging due to the combinatorial number of possible states of the population. Moreover, while the modeller easily hypothesises the mechanistic aspects of the model, the quantitative parameters associated to these mechanistic transitions are difficult or impossible to measure directly. In this paper, we investigate how formal verification methods can aid parameter inference for population discrete-time Markov chains in a scenario where only a limited sample of population-level data measurements—sample distributions among terminal states—are available. We first discuss the parameter identifiability and uncertainty quantification in this setup, as well as how the existing techniques of formal parameter synthesis and Bayesian inference apply. Then, we propose and implement four different methods, three of which incorporate formal parameter synthesis as a pre-computation step. We empirically evaluate the performance of the proposed methods over four representative case studies. We find that our proposed methods incorporating formal parameter synthesis as a pre-computation step allow us to significantly enhance the accuracy, precision, and scalability of inference. Specifically, in the case of unidentifiable parameters, we accurately capture the subspace of parameters which is data-compliant at a desired confidence level.