bluuebunny/crossref_metadata_2025 huggingface dataset:
Bayesian multi-exposure image fusion for robust high dynamic range ptychography
Authors: Kodgirwar Shantanu , Loetgering Lars , Liu Chang , Joseph Aleena , Licht Leona , Penagos Molina Daniel S. , Eschen Wilhelm , Rothhardt Jan , Habeck Michael
Published: May 2024

The limited dynamic range of the detector can impede coherent diffractive imaging (CDI) schemes from achieving diffraction-limited resolution. To overcome this limitation, a straightforward approach is to utilize high dynamic range (HDR) imaging through multi-exposure image fusion (MEF). This method involves capturing measurements at different exposure times, spanning from under to overexposure and fusing them into a single HDR image. The conventional MEF technique in ptychography typically involves subtracting the background noise, ignoring the saturated pixels and then merging the acquisitions. However, this approach is inadequate under conditions of low signal-to-noise ratio (SNR). Additionally, variations in illumination intensity significantly affect the phase retrieval process. To address these issues, we propose a Bayesian MEF modeling approach based on a modified Poisson distribution that takes the background and saturation into account. The expectation-maximization (EM) algorithm is employed to infer the model parameters. As demonstrated with synthetic and experimental data, our approach outperforms the conventional MEF method, offering superior phase retrieval under challenging experimental conditions. This work underscores the significance of robust multi-exposure image fusion for ptychography, particularly in imaging shot-noise-dominated weakly scattering specimens or in cases where access to HDR detectors with high SNR is limited. Furthermore, the applicability of the Bayesian MEF approach extends beyond CDI to any imaging scheme that requires HDR treatment. Given this versatility, we provide the implementation of our algorithm as a Python package.
Chiral photon blockade in the spinning Kerr resonator
Authors: Zuo Yunlan , Jiao Ya-Feng , Xu Xun-Wei , Miranowicz Adam , Kuang Le-Man , Jing Hui
Published: May 2024

We propose how to achieve chiral photon blockade by spinning a nonlinear optical resonator. We show that by driving such a device at a fixed direction, completely different quantum effects can emerge for the counter-propagating optical modes, due to the spinning-induced breaking of time-reversal symmetry, which otherwise is unattainable for the same device in the static regime. Also, we find that in comparison with the static case, robust non-classical correlations against random backscattering losses can be achieved for such a quantum chiral system. Our work, extending previous works on the spontaneous breaking of optical chiral symmetry from the classical to purely quantum regimes, can stimulate more efforts towards making and utilizing various chiral quantum effects, including applications for chiral quantum networks or noise-tolerant quantum sensors.
Rotational angle and speed detection via a chip-scale GaN optoelectronic device
Authors: Shi Fan , Jiang Chengxiang , Fang Li , Sun Zhihang , Yan Jiabin , Shi Zheng , Zhu Hongbo , Wang Yongjin
Published: May 2024

In this paper, a new method for rotational angle and speed measurements is proposed by integrating a GaN optoelectronic chip with a stepped disc. The optoelectronic chip that integrates a light-emitting diode (LED) and a photodiode (PD) is fabricated by wafer-level microfabrication. The disc is designed with a spiral staircase shape, and has increasing thickness distribution along the circumferential direction. The sensing mechanism is that the optoelectronic chip measures angle-dependent intensity change of the light reflected off the stepped disc. Through a series of performance tests, the chip is highly sensitive to a continuous rotation from 0∘ to 360∘, and produces photocurrent to indicate the rotational angle and speed. A rotational speed up to 5000 rpm is measured with a relative error less than 1.27%. The developed sensing architecture provides an alternative solution for constructing a low-cost, miniaturized, and high-efficiency rotational angle and speed sensing system.
High-quality quasi-bound state in the continuum enabled single-nanoparticle virus detection
Authors: Li Zonglin , Nie Guozheng , Chen Ziqi , Zhan Shiping , Lan Linfeng
Published: May 2024

Bound states in the continuum (BICs) have emerged as a powerful platform for boosting light–matter interactions because they provide an alternative way of realizing optical resonances with ultrahigh quality(Q-) factors, accompanied by extreme field confinement. In this work, we realized an optical biosensor by introducing a quasi-BIC (qBIC) supported by an elaborated all-dielectric dimer grating. Thanks to the excellent field confinement within the air gap of grating enabled by such a high-Q qBIC, the figure of merit (FOM) of a biosensor is up to 18,908.7 RIU−1. Furthermore, we demonstrated that such a high-Q grating can help push the limit of optical biosensing to the single-particle level. Our results may find exciting applications in extreme biochemical sensing like COVID-19 with ultralow concentration.
Distributed shape detection for an acoustic sensitive optical cable with DAS
Authors: Chen Boqi , Wang Zhaoyong , Yang Junqi , Liu Yifan , Chen Yici , Wu Jinyi , Gao Kan , Ye Qing
Published: May 2024

Acoustic sensitive optical cables (ASOCs) and their shape detection are vital in underwater acoustic monitoring, and a distributed ASOC shape detection method is demonstrated with distributed acoustic sensing (DAS) technology. The accurate three-dimensional (3D) position of each ASOC unit is obtained from DAS signals and the prior position information of auxiliary acoustic sources by using a proposed adaptive peak allocation algorithm. Preliminary work has demonstrated single-point 3D localization and distributed ASOC shape detection, and the error is 6.53 cm. To the best of our knowledge, it is the first time that distributed ASOC shape detection is achieved with DAS. This method will promote the development of ASOC applications, such as underwater target detection and towed array correction.
Lever-enabled milli-Newton mechanical force detection via a microbottle resonator
Authors: Wang Zijie , Zhang Xiaobei , Zhang Qi , Cao Zong , Yang Yong , Wang Tingyun
Published: May 2024

We demonstrate a milli-Newton mechanical force sensor based on a whispering gallery mode microbottle resonator (MBR). A lever model is established by coupling the MBR with a tapered fiber, whose ratio of load arm to effort arm (RLE) is flexibly adjusted to enlarge the detection range. The mechanical force is induced by attaching a capillary on the MBR stem and applying the downward displacement, which deforms the MBR’s radius and thus shifts the resonance wavelength. The dependence of the capillary displacement on the mechanical force is theoretically deduced and verified. Experimentally, the sensors with different RLEs are built, and the maximum sensitivity of −10.48 pm/mN with a resolution of 40 µN is obtained. The achieved detection range is 0–4 mN, which depends on the capillary displacement and RLE of the lever. With the merits of easy fabrication and flexible structure, the proposed sensor shows great potential in biomedical and structural health monitoring.
Thin-film lithium niobate-based electro-optic comb cloning for self-homodyne coherent communication
Authors: Liu Xu , Zhang Chenbo , Lin Jingjing , He Bibo , Chen Nuo , He Xuanjian , Chu Tao , Chen Zhangyuan , Hu Weiwei , Xie Xiaopeng
Published: May 2024

As the optical communication industry advances, metropolitan area networks (MANs) and radio access networks (RANs) are extensively deployed on a large scale, demanding energy-efficient integrated light sources and simplified digital signal processing (DSP) technologies. The emergence of thin-film lithium niobate (TFLN) has given rise to high-performance, energy-efficient on-chip modulators, making on-chip optical frequency comb (OFC) more appealing. Owing to the phase uniformity and stability of this chip-scale device, it has been possible to eliminate the carrier frequency phase estimation (CPE) in DSP stacks using comb-clone-enabled self-homodyne detection. Here we report the first use, to our knowledge, of a TFLN on-chip electro-optic (EO) frequency comb to realize comb cloning and self-homodyne coherent detection. We transmit three optical pilot tones and eight data channels encoded with 20 Gbaud polarization-multiplexed 16-ary quadrature amplitude modulation (PM-16-QAM) over 10 km and 80 km standard single-mode fibers. The bit error ratios (BERs) of the eight channels reach below 10−3, a result made possible by our on-chip comb. The scalability and mass producibility of on-chip EO combs, combined with the simplified DSP, show potential in our proposed fifth-generation (5G) RAN and MAN transmission scheme.
Alkenyl oxindole is a novel PROTAC moiety that recruits the CRL4DCAF11 E3 ubiquitin ligase complex for targeted protein degradation
Authors: Wang Ying , Wei Tianzi , Zhao Man , Huang Aima , Sun Fan , Chen Lu , Lin Risheng , Xie Yubao , Zhang Ming , Xu Shiyu , Sun Zhihui , Hong Liang , Wang Rui , Tian Ruilin , Li Guofeng
Published: May 2024

Alkenyl oxindoles have been characterized as autophagosome-tethering compounds (ATTECs), which can target mutant huntingtin protein (mHTT) for lysosomal degradation. In order to expand the application of alkenyl oxindoles for targeted protein degradation, we designed and synthesized a series of heterobifunctional compounds by conjugating different alkenyl oxindoles with bromodomain-containing protein 4 (BRD4) inhibitor JQ1. Through structure-activity relationship study, we successfully developed JQ1-alkenyl oxindole conjugates that potently degrade BRD4. Unexpectedly, we found that these molecules degrade BRD4 through the ubiquitin-proteasome system, rather than the autophagy-lysosomal pathway. Using pooled CRISPR interference (CRISPRi) screening, we revealed that JQ1-alkenyl oxindole conjugates recruit the E3 ubiquitin ligase complex CRL4DCAF11 for substrate degradation. Furthermore, we validated the most potent heterobifunctional molecule HL435 as a promising drug-like lead compound to exert antitumor activity both in vitro and in a mouse xenograft tumor model. Our research provides new employable proteolysis targeting chimera (PROTAC) moieties for targeted protein degradation, providing new possibilities for drug discovery.
A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens
Authors: Choudhery Sanjeevani , DeJesus Michael A. , Srinivasan Aarthi , Rock Jeremy , Schnappinger Dirk , Ioerger Thomas R.
Published: May 2024

An important application of CRISPR interference (CRISPRi) technology is for identifying chemical-genetic interactions (CGIs). Discovery of genes that interact with exposure to antibiotics can yield insights to drug targets and mechanisms of action or resistance. The objective is to identify CRISPRi mutants whose relative abundance is suppressed (or enriched) in the presence of a drug when the target protein is depleted, reflecting synergistic behavior. Different sgRNAs for a given target can induce a wide range of protein depletion and differential effects on growth rate. The effect of sgRNA strength can be partially predicted based on sequence features. However, the actual growth phenotype depends on the sensitivity of cells to depletion of the target protein. For essential genes, sgRNA efficiency can be empirically measured by quantifying effects on growth rate. We observe that the most efficient sgRNAs are not always optimal for detecting synergies with drugs. sgRNA efficiency interacts in a non-linear way with drug sensitivity, producing an effect where the concentration-dependence is maximized for sgRNAs of intermediate strength (and less so for sgRNAs that induce too much or too little target depletion). To capture this interaction, we propose a novel statistical method called CRISPRi-DR (for Dose-Response model) that incorporates both sgRNA efficiencies and drug concentrations in a modified dose-response equation. We use CRISPRi-DR to re-analyze data from a recent CGI experiment in Mycobacterium tuberculosis to identify genes that interact with antibiotics. This approach can be generalized to non-CGI datasets, which we show via an CRISPRi dataset for E. coli growth on different carbon sources. The performance is competitive with the best of several related analytical methods. However, for noisier datasets, some of these methods generate far more significant interactions, likely including many false positives, whereas CRISPRi-DR maintains higher precision, which we observed in both empirical and simulated data.
A multimodal Transformer Network for protein-small molecule interactions enhances predictions of kinase inhibition and enzyme-substrate relationships
Authors: Kroll Alexander , Ranjan Sahasra , Lercher Martin J.
Published: May 2024

The activities of most enzymes and drugs depend on interactions between proteins and small molecules. Accurate prediction of these interactions could greatly accelerate pharmaceutical and biotechnological research. Current machine learning models designed for this task have a limited ability to generalize beyond the proteins used for training. This limitation is likely due to a lack of information exchange between the protein and the small molecule during the generation of the required numerical representations. Here, we introduce ProSmith, a machine learning framework that employs a multimodal Transformer Network to simultaneously process protein amino acid sequences and small molecule strings in the same input. This approach facilitates the exchange of all relevant information between the two molecule types during the computation of their numerical representations, allowing the model to account for their structural and functional interactions. Our final model combines gradient boosting predictions based on the resulting multimodal Transformer Network with independent predictions based on separate deep learning representations of the proteins and small molecules. The resulting predictions outperform recently published state-of-the-art models for predicting protein-small molecule interactions across three diverse tasks: predicting kinase inhibitions; inferring potential substrates for enzymes; and predicting Michaelis constants KM. The Python code provided can be used to easily implement and improve machine learning predictions involving arbitrary protein-small molecule interactions.
A computational analysis of the role of integrins and Rho-GTPases in the emergence and disruption of apical-basal polarization in renal epithelial cells
Authors: Hagelaars Maria J. , Nikolic Milica , Vermeulen Maud , Dekker Sylvia , Bouten Carlijn V. C. , Loerakker Sandra
Published: May 2024

Apical-basal polarization in renal epithelial cells is crucial to renal function and an important trigger for tubule formation in kidney development. Loss of polarity can induce epithelial-to-mesenchymal transition (EMT), which can lead to kidney pathologies. Understanding the relative and combined roles of the involved proteins and their interactions that govern epithelial polarity may provide insights for controlling the process of polarization via chemical or mechanical manipulations in an in vitro or in vivo setting. Here, we developed a computational framework that integrates several known interactions between integrins, Rho-GTPases Rho, Rac and Cdc42, and polarity complexes Par and Scribble, to study their mutual roles in the emergence of polarization. The modeled protein interactions were shown to induce the emergence of polarized distributions of Rho-GTPases, which in turn led to the accumulation of apical and basal polarity complexes Par and Scribble at their respective poles, effectively recapitulating polarization. Our multiparametric sensitivity analysis suggested that polarization depends foremost on the mutual inhibition between Rac and Rho. Next, we used the computational framework to investigate the role of integrins and GTPases in the generation and disruption of polarization. We found that a minimum concentration of integrins is required to catalyze the process of polarization. Furthermore, loss of polarization was found to be only inducible via complete degradation of the Rho-GTPases Rho and Cdc42, suggesting that polarization is fairly stable once it is established. Comparison of our computational predictions against data from in vitro experiments in which we induced EMT in renal epithelial cells while quantifying the relative Rho-GTPase levels, displayed that EMT coincides with a large reduction in the Rho-GTPase Rho. Collectively, these results demonstrate the essential roles of integrins and Rho-GTPases in the establishment and disruption of apical-basal polarity and thereby provide handles for the in vitro or in vivo regulation of polarity.
C-reactive protein and high-sensitivity C-reactive protein levels in asymptomatic intestinal parasite carriers from urban and rural areas of Gabon
Authors: Kono Helena Noéline , Ada Mengome Mérédith Flore , Pongui Ngondza Bedrich , Sibi Matotou Roger Hadry , Ndong Akomezoghe Luccheri , Ekomi Bernadette , Moutombi Ditombi Bridy Chesly , Koumba Lengongo Jeanne Vanessa , Ndong Ngomo Jacques Mari , M’Bondoukwé Noé Patrick , Bisseye Cyrille , Mawili-Mboumba Denise Patricia , Bouyou Akotet Marielle Karine
Published: May 2024

Background

Chronic carriage of intestinal parasitic infections (IPIs) can induce chronic inflammation and dysbiosis, which are risk factors for non-communicable diseases. The objective of this study was to determine the relationship between IPI carriage and inflammation in a population of volunteers living in Gabon.

Methodology and principal findings

A cross-sectional study was conducted from September 2020 to November 2021 in asymptomatic volunteers aged 18 years old and over, residing in different areas of Gabon: Libreville (urban area) and Koula-Moutou and Bitam (rural areas). The detection of IPIs was carried out using four common microscopic techniques. C-reactive protein (CRP), and high-sensitivity C-reactive protein (hsCRP) were measured and levels were compared according to the presence or absence of IPI. Overall, 518 participants were included, 64.5% (n = 334) of whom resided in urban area and 35.5% (n = 184) in rural areas. The median age was 35 years (27; 46). The prevalence of asymptomatic IPIs was 29.9% (n = 155), with a significantly higher frequency in rural areas than in urban area (adjusted OR 6.6 (CI 3.2–13.8), p < 0.01). Protozoa were more frequent than soil-transmitted helminths (STHs) in both areas: 81.6% (n = 40) in urban area and 69.8% (n = 74) in rural areas. STHs were predominant in rural areas (48.1% vs 22.4% in urban area. In case of IPI, the median values of CRP (15 (13–15) mg/L vs 13.0 (11.1–14.9) mg/L) and hsCRP (4.2 (1.4–13.0) mg/L vs 2.2(0.4–6.1) mg/L) were higher (p<0.01). Elevated hsCRP and CRP were significantly more frequent in parasitized individuals (for hsCRP: 22.6%, n = 35; for CRP: 52.9%, n = 82); in particular among STH carriers (for hsCRP: 65.9%, n = 27, for CRP: 36.6%, n = 15) (p < 0.01).

Conclusions/Significance

This first study showed that asymptomatic IPIs, particularly STH carriage are associated with high CRP and hsCRP levels. Further larger and longitudinal studies are needed to elucidate the global and specie-specific enteropathogens link with chronic inflammation.
Evolution of rarity and phylogeny determine above- and belowground biomass in plant-plant interactions
Authors: Nytko Alivia G. , Hord Ashlynn M. , Senior John K. , O’Reilly-Wapstra Julianne , Schweitzer Jennifer A. , Bailey Joseph K.
Published: May 2024

Rare species are often considered inferior competitors due to occupancy of small ranges, specific habitats, and small local populations. However, the phylogenetic relatedness and rarity level (level 1–7 and common) of interacting species in plant-plant interactions are not often considered when predicting the response of rare plants in a biotic context. We used a common garden of 25 species of Tasmanian Eucalyptus, to differentiate non-additive patterns in the biomass of rare versus common species when grown in mixtures varying in phylogenetic relatedness and rarity. We demonstrate that rare species maintain progressively positive non-additive responses in biomass when interacting with phylogenetically intermediate, less rare and common species. This trend is not reflected in common species that out-performed in monocultures compared to mixtures. These results offer predictability as to how rare species’ productivity will respond within various plant-plant interactions. However, species-specific interactions, such as those involving E. globulus, yielded a 97% increase in biomass compared to other species-specific interaction outcomes. These results are important because they suggest that plant rarity may also be shaped by biotic interactions, in addition to the known environmental and population factors normally used to describe rarity. Rare species may utilize potentially facilitative interactions with phylogenetically intermediate and common species to escape the effects of limiting similarity. Biotically mediated increases in rare plant biomass may have subsequent effects on the competitive ability and geographic occurrence of rare species, allowing rare species to persist at low abundance across plant communities. Through the consideration of species rarity and evolutionary history, we can more accurately predict plant-plant interaction dynamics to preserve unique ecosystem functions and fundamentally challenge what it means to be “rare”.
An integrated group decision-making method under q-rung orthopair fuzzy 2-tuple linguistic context with partial weight information
Authors: Abbas Fatima , Ali Jawad , Mashwani Wali Khan , Syam Muhammad I.
Published: May 2024

Considering the advantages of q-rung orthopair fuzzy 2-tuple linguistic set (q-RFLS), which includes both linguistic and numeric data to describe evaluations, this article aims to design a new decision-making methodology by integrating Vlsekriterijumska Optimizacija I Kompromisno Resenje (VIKOR) and qualitative flexible (QUALIFLEX) methods based on the revised aggregation operators to solve multiple criteria group decision making (MCGDM). To accomplish this, we first revise the extant operational laws of q-RFLSs to make up for their shortcomings. Based on novel operational laws, we develop q-rung orthopair fuzzy 2-tuple linguistic (q-RFL) weighted averaging and geometric operators and provide the corresponding results. Next, we develop a maximization deviation model to determine the criterion weights in the decision-making procedure, which accounts for partial weight unknown information. Then, the VIKOR and QUALIFLEX methodologies are combined, which can assess the concordance index of each ranking combination using group utility and individual maximum regret value of alternative and acquire the ranking result based on each permutation’s general concordance index values. Consequently, a case study is conducted to select the best bike-sharing recycling supplier utilizing the suggested VIKOR-QUALIFLEX MCGDM method, demonstrating the method’s applicability and availability. Finally, through sensitivity and comparative analysis, the validity and superiority of the proposed method are demonstrated.
Implementation of the My Abilities First Tool: A qualitative study on the perceptions of professionals, caregivers, children, and adolescents with disabilities
Authors: Alencar Roselene F. , Longo Egmar , Schiariti Verónica , Jesus Caline C. A. F. , Carrión Rocío P. , Alvarez Carolina D. L. , Coelho Monique L. G. , Pereira Tatiana F. C. , Cruz Maria C. L. , Melgão Sanzia S. V. , Lindquist Ana Raquel R.
Published: May 2024

Objective

To analyze the perceptions of professionals, caregivers, children, and adolescents with disabilities regarding the implementation of the My Abilities First (MAF) tool in Specialized Child Rehabilitation Centers (CERs).

Method

This is a qualitative research based on Reflexive Thematic Analysis (RTA). The study involved twenty-seven intentionally selected individuals, comprising 12 physiotherapists, 4 occupational therapists, 11 caregivers, 9 children and 2 adolescents. Participants completed sociodemographic and clinical questionnaires and took part in semi-structured online interviews, focusing on two themes: Positive health approaches and the MAF tool. The study was approved by the local ethics committee (opinion 4.779.175).

Results

Reflexive Thematic Analysis of the interviews resulted in two themes: (1) Perceptions regarding the MAF tool as an educational and contributory process to enhance the inclusion and participation of children and adolescents with disabilities, and (2) Barriers and facilitators for the implementation process of the MAF tool. The implementation of MAF was identified as a driving factor in promoting equity and increased participation of children and adolescents with disabilities in various settings, including health, education, and leisure. Interviewees highlighted the need to confront attitudinal, communication, and social barriers that may hinder the implementation of the tool.

Conclusion

The implementation of the MAF tool was perceived as an innovation due to its focus on the abilities of individuals with disabilities. However, there is a need to restructure it to broaden its scope and access to different contexts in order to confront barriers and enhance the inclusion and participation of children and adolescents with disabilities.
The impact of gendered experiences on the career choice of swiss medical students: A qualitative study protocol
Authors: Arnoux Sylvie , Hirshfield Laura E. , Abbiati Milena , Nendaz Mathieu R. , Savoldelli Georges L. , Bajwa Nadia M.
Published: May 2024

The problem of gender discrimination and sexual harassment in medicine is long-standing and widespread. This project aims to document and understand how gendered experiences encountered by final-year medical students in Switzerland are experienced by these individuals and how they influence their career choice. It also aims to identify representations and stereotypes linked to the different specialties. The project will take place at all Swiss universities offering a master’s degree in human medicine, for a total of 9 programs. Around 36 participants will be recruited. Semi-structured qualitative individual interviews will be conducted. Analysis will be based on Grounded Theory principles.
How does China’s green credit policy affect the innovation of high-polluting enterprises? From the perspective of innovation quantity and quality
Authors: Bai E. , Wu Kai , Zhu Hongxin , Zhu Hejie , Lu Zhijiang
Published: May 2024

Employing the “Green Credit Guidelines” implemented in 2012 as the basis for a quasi-natural experiment, this study applies the method of Difference-in-Differences(DID) to investigate the influence of the Green Credit Policy on both the quantity and quality of enterprise innovation. The outcomes of our analysis reveal that the policy has significantly boosted both the quantity and quality of innovation among enterprises identified as heavy polluters. It is noteworthy that the policy’s positive impact on innovation quantity surpasses its positive effect on innovation quality. This substantiates that the Green Credit Policy effectively generates incentivizing outcomes for innovation among the heavy polluters, thereby verifying Porter’s hypothesis within the domain of green credit in China. Furthermore, we find that the positive impact is more significant for enterprises with lower innovation capabilities, large-scale enterprises, state-owned enterprises, and those situated in both the Eastern and Western regions. Through these findings, this study illuminates a novel perspective on the interplay between the Green Credit Policy and enterprise innovation dynamics in China.
Citizen scientists: Unveiling motivations and characteristics influencing initial and sustained participation in an agricultural project
Authors: Vanden Berghen Birgit , Vanermen Iris , Vranken Liesbet
Published: May 2024

Citizen science, where non-specialists collaborate with scientists, has surged in popularity. While it offers an innovative approach to research involvement, the domain of agri-environmental research participation, particularly in terms of citizen recruitment and retention, remains relatively unexplored. To investigate how what factors influence initial and sustained participation in an agronomic citizen science project, we performed a large survey during the case-study “Soy in 1000 Gardens”. We obtained data on citizens motivations, general values, environmental concern, prior citizen science experience, and knowledge regarding sustainable food consumption and garden management and applied a two-step selection model to correct for potential self-selection bias on our participation outcomes. Initially, citizen scientists appear to be mostly motivated by gaining knowledge, having fun social interactions and environmental concern with regards to the effects on others, while the desire for enhancing or protecting their ego is less prominent. They also display higher knowledge and self-transcending values. Sustained participants however, are significantly older and share a stronger sense of moral obligation than their dropped-out counterparts. Moreover, prior experience seems to positively influence the length of their participation, while higher knowledge has a positive impact on the amount of data contributed. These insights offer strategies for tailored engagement that should emphasize collective impact, align with intrinsic values, and foster a sense of moral duty, with potential to enhance agri-environmental citizen science initiatives’ effectiveness in addressing environmental challenges.
Selenium intake in relation to all-cause and cardiovascular mortality in individuals with nonalcoholic fatty liver disease: A nationwide study in nutrition
Authors: Dong Xin , Deng Yunchao , Chen Gang
Published: May 2024

Aims

Limited evidence exists regarding the association of selenium with risk of death in individuals with nonalcoholic fatty liver disease (NAFLD). This study was designed to investigate the relationship between dietary selenium intake with mortality in a nationally representative sample of United States adults with NAFLD.

Methods

Dietary selenium intake was assessed in 2274 NAFLD adults younger than 60 years of age from the National Health and Nutrition Examination Survey (NHANES) III through a 24-hour dietary recall. NAFLD was diagnosed by liver ultrasound after excluding liver disease due to other causes. Cox proportional hazards models were utilized to assess the effect of dietary selenium intake on all-cause and cardiovascular mortality among individuals with NAFLD.

Results

At a median follow-up of 27.4 years, 577 deaths occurred in individuals with NAFLD, including 152 cardiovascular deaths. The U-shaped associations were discovered between selenium intake with all-cause (Pnolinear = 0.008) and cardiovascular mortality (Pnolinear < 0.001) in adults with NAFLD after multivariate adjustment, with the lowest risk around selenium intake of 121.7 or 125.9 μg/day, respectively. Selenium intake in the range of 104.1–142.4 μg/day was associated with a reduced risk of all-cause mortality and, otherwise, an increased risk. Selenium intake in the range of 104.1–150.6 μg/day was associated with a reduced risk of cardiovascular death and, otherwise, an increased risk.

Conclusions

Both high and low selenium intake increased the risk of all-cause and cardiovascular death in adults younger than 60 years of age with NAFLD, which may help guide dietary adjustments and improve outcomes in adults with NAFLD.
An NGS-based assay for accurate detection and quantification of immune gene expression in mouse tumor models
Authors: Xue Jia , Chen Xiaobo , An Xiaoyu , Wang Jingjing , Zang Mingfa , Mao Binchen , Guo Sheng , Yang Tao , Kumari Rajendra , Li Qi-Xiang
Published: May 2024

Tumor microenvironment (TME) is a complex dynamic system with many tumor-interacting components including tumor-infiltrating leukocytes (TILs), cancer associated fibroblasts, blood vessels, and other stromal constituents. It intrinsically affects tumor development and pharmacology of oncology therapeutics, particularly immune-oncology (IO) treatments. Accurate measurement of TME is therefore of great importance for understanding the tumor immunity, identifying IO treatment mechanisms, developing predictive biomarkers, and ultimately, improving the treatment of cancer. Here, we introduce a mouse-IO NGS-based (NGSmIO) assay for accurately detecting and quantifying the mRNA expression of 1080 TME related genes in mouse tumor models. The NGSmIO panel was shown to be superior to the commonly used microarray approach by hosting 300 more relevant genes to better characterize various lineage of immune cells, exhibits improved mRNA and protein expression correlation to flow cytometry, shows stronger correlation with mRNA expression than RNAseq with 10x higher sequencing depth, and demonstrates higher sensitivity in measuring low-expressed genes. We describe two studies; firstly, detecting the pharmacodynamic change of interferon-γ expression levels upon anti-PD-1: anti-CD4 combination treatment in MC38 and Hepa 1–6 tumors; and secondly, benchmarking baseline TILs in 14 syngeneic tumors using transcript level expression of lineage specific genes, which demonstrate effective and robust applications of the NGSmIO panel.
Exploring pathogenesis and biomarkers through establishment of a rat model of male infertility with liver depression and kidney deficiency
Authors: Shen Ying , Fan Jian , Liu Shaobo , Tao Ling , Yang Qingbo , Shen Xiangchun
Published: May 2024

Objectives

To establish a rat model that accurately replicates the clinical characteristics of male infertility (MI) with Liver Depression and Kidney Deficiency (LD & KD) and investigate the pathogenesis.

Methods

After subjecting the rats to chronic restraint stress (CRS) and adenine treatment, a series of tests were conducted, including ethological assessments, evaluations of reproductive characteristics, measurements of biochemical parameters, histopathological examinations, and analyses of urinary metabolites. Additionally, bioinformatics predictions were performed for comprehensive analysis.

Results

Compared to the control, the model exhibited significant manifestations of MI with LD & KD, including reduced responsiveness, diminished frequency of capturing estrous female rats, and absence of mounting behavior. Additionally, the kidney coefficient increased markedly, while the coefficients of the testis and epididymis decreased significantly. Sperm counts and viabilities decreased notably, accompanied by an increase in sperm abnormalities. Dysregulation of reproductive hormone levels in the serum was observed, accompanied by an upregulation of proinflammatory cytokines expressions in the liver and kidney, as well as exacerbated oxidative stress in the penile corpus cavernosum and testis. The seminiferous tubules in the testis exhibited a loose arrangement, loss of germ cells, and infiltration of inflammatory cells. Furthermore, utilizing urinary metabolomics and bioinformatics analysis, 5 key biomarkers and 2 crucial targets most closely linked to MI were revealed.

Conclusion

The study successfully established a clinically relevant animal model of MI with LD & KD. It elucidates the pathogenesis of the condition, identifies key biomarkers and targets, and provides a robust scientific foundation for the prediction, diagnosis, and treatment of MI with LD & KD.
Visualising and quantifying the usefulness of new predictors stratified by outcome class: The U-smile method
Authors: Kubiak Katarzyna B. , Więckowska Barbara , Jodłowska-Siewert Elżbieta , Guzik Przemysław
Published: May 2024

Binary classification methods encompass various algorithms to categorize data points into two distinct classes. Binary prediction, in contrast, estimates the likelihood of a binary event occurring. We introduce a novel graphical and quantitative approach, the U-smile method, for assessing prediction improvement stratified by binary outcome class. The U-smile method utilizes a smile-like plot and novel coefficients to measure the relative and absolute change in prediction compared with the reference method. The likelihood-ratio test was used to assess the significance of the change in prediction. Logistic regression models using the Heart Disease dataset and generated random variables were employed to validate the U-smile method. The receiver operating characteristic (ROC) curve was used to compare the results of the U-smile method. The likelihood-ratio test demonstrated that the proposed coefficients consistently generated smile-shaped U-smile plots for the most informative predictors. The U-smile plot proved more effective than the ROC curve in comparing the effects of adding new predictors to the reference method. It effectively highlighted differences in model performance for both non-events and events. Visual analysis of the U-smile plots provided an immediate impression of the usefulness of different predictors at a glance. The U-smile method can guide the selection of the most valuable predictors. It can also be helpful in applications beyond prediction.
Preanalytical considerations for clinical assays of circulating human miRNA-451a, miRNA-423-5p and miRNA-199a-3p for diagnostic purposes
Authors: Chandel Dinesh S. , Tom Wesley A. , Jiang Chao , Krzyzanowski Gary , Fernando Nirmalee , Olou Appolinaire , Fernando M. Rohan
Published: May 2024

Circulating miRNA has recently emerged as important biomolecules with potential clinical values as diagnostic markers for several diseases. However, to be used as such, it is critical to accurately quantify miRNAs in the clinic. Yet, preanalytical factors that can affect an error-free quantification of these miRNAs have not been explored. This study aimed at investigating several of these preanalytical factors that may affect the accurate quantification of miRNA-451a, miRNA-423-5p and miRNA-199a-3p in human blood samples. We initially evaluated levels of these three miRNAs in red blood cells (RBCs), white blood cells (WBCs), platelets, and plasma by droplet digital PCR (ddPCR). Next, we monitored miRNA levels in whole blood or platelet rich plasma (PRP) stored at different temperatures for different time periods by ddPCR. We also investigated the effects of hemolysis on miRNA concentrations in platelet-free plasma (PFP). Our results demonstrate that more than 97% of miRNA-451a and miRNA-423-5p in the blood are localized in RBCs, with only trace amounts present in WBCs, platelets, and plasma. Highest amount of the miRNA-199a-3p is present in platelets. Hemolysis had a significant impact on both miRNA-451a and miRNA-423-5p concentrations in plasma, however miRNA-199a levels remain unaffected. Importantly, PRP stored at room temperature (RT) or 4°C showed a statistically significant decrease in miRNA-451a levels, while the other two miRNAs were increased, at days 1, 2, 3 and 7. PFP at RT caused statistically significant steady decline in miRNA-451a and miRNA-423-5p, observed at 12, 24, 36, 48 and 72 hours. Levels of the miRNA-199a-3p in PFP was stable during first 72 hours at RT. PFP stored at -20°C for 7 days showed declining stability of miRNA-451a over time. However, at -80°C miRNA-451a levels were stable up to 7 days. Together, our data indicate that hemolysis and blood storage at RT, 4°C and -20°C may have significant negative effects on the accuracy of circulating miRNA-451a and miRNA-423-5p quantification.
A national audit of facilities, human and material resources for the comprehensive management of diabetes in Ghana-A 2023 update
Authors: Yorke Ernest , Akpalu Josephine , de-Graft Johnson Gwendolyn , Atiase Yacoba , Reynolds Margaret , Laryea Ruth , Tetteh John , Yawson Alfred E. , Amoah Albert G. B.
Published: May 2024

Introduction

The human and material resources as well as the systems for managing diabetes in Africa are inadequate. This study or needs assessment, aimed at updating the human and material resources, identifying the gaps and unmet needs for comprehensive diabetes care in Ghana.

Methods

We conducted a national audit of 122 facilities in all 16 administrative regions of Ghana. Information obtained covered areas on personnel and multidisciplinary teams, access to medications, access to laboratory services, financing, screening services, management of diabetes complications, and availability/use of diabetes guidelines or protocols. Data was analysed using STATA version 16.1. P-values <0.05 were set as significant.

Results

Only 85(69.7%) out of the 122 surveyed facilities had a dedicated centre or service for diabetes care. Twenty-eight (23%) had trained diabetes doctors/specialists; and whilst most centres had ophthalmic nurses and dieticians, majority of them did not have trained diabetes educators (nurses), psychologists, ophthalmologists, podiatrists, and foot/vascular surgeons. Also, 13.9% had monofilaments, none could perform urine dipstick for microalbumin; 5 (4.1%) and just over 50% could perform laboratory microalbumin estimation and glycated haemoglobin, respectively. Access to and supply of human insulins was better than analogue insulin in most centres. Nearly 100% of the institutions surveyed had access to metformin and sulphonylurea with good to excellent supply in most cases, whilst access to Sodium Glucose Transporter-2 inhibitors and Glucagon-like peptide-1 analogues were low, and moderate for Dipeptidyl peptidase-4 inhibitors and thiazolidinediones. Majority of the health facilities (95.1%) offered NHIS as payment mechanism for clients, whilst 68.0% and 30.3% of the patients paid for services using out-of-pocket and private insurance respectively. Fifteen facilities (12.3%) had Diabetes Support Groups in their locality and catchment areas.

Conclusion

An urgent multisectoral collaboration, including prioritisation of resources at the facility level, to promote and achieve acceptable comprehensive diabetes care is required.
Genome-wide screening of meta-QTL and candidate genes controlling yield and yield-related traits in barley (Hordeum vulgare L.)
Authors: Du Binbin , Wu Jia , Wang Qingming , Sun Chaoyue , Sun Genlou , Zhou Jie , Zhang Lei , Xiong Qingsong , Ren Xifeng , Lu Baowei
Published: May 2024

Increasing yield is an important goal of barley breeding. In this study, 54 papers published from 2001–2022 on QTL mapping for yield and yield-related traits in barley were collected, which contained 1080 QTLs mapped to the barley high-density consensus map for QTL meta-analysis. These initial QTLs were integrated into 85 meta-QTLs (MQTL) with a mean confidence interval (CI) of 2.76 cM, which was 7.86-fold narrower than the CI of the initial QTL. Among these 85 MQTLs, 68 MQTLs were validated in GWAS studies, and 25 breeder’s MQTLs were screened from them. Seventeen barley orthologs of yield-related genes in rice and maize were identified within the hcMQTL region based on comparative genomics strategy and were presumed to be reliable candidates for controlling yield-related traits. The results of this study provide useful information for molecular marker-assisted breeding and candidate gene mining of yield-related traits in barley.
Subjective perception of visual field defects using random noise-moving images in patients with glaucoma: A comparison of computer graphics and analog noises
Authors: Inoue Arata , Koike Eiko , Maeda Naoyuki , Matsumoto Chota
Published: May 2024

Purpose

Random noise-moving images (noises) can make glaucoma patients with no subjective symptoms aware of visual field abnormalities. To explore this concept, we developed a noise using computer graphics (CG) and investigated the difference in the subjective perception of visual field abnormalities between CG and conventional analog noises.

Methods

We enrolled individuals with glaucoma (205 eyes), preperimetric glaucoma (PPG; 19 eyes), and normal eyes (35 eyes). For a CG noise, a series of still images was made by randomly selecting five monochromatic tones on 2-mm square dots, and these images were drawn at 60 frames per second (fps) to create a noise-moving image. The participants were asked to describe their perceived shadows on a paper. The results were categorized as follows based on the pattern deviation probability map of the Humphrey field analyzer (HFA): “agreement,” “partial agreement,” “disagreement,” and “no response.” The glaucoma stage was classified into four stages, from M1 to M4, based on the HFA’s mean deviation.

Result

The detection rates (agreement and partial agreement) were 80.5% and 65.4% for the CG and analog noises, respectively, with CG noise showing a significantly higher detection rate in all glaucoma eyes (P < 0.001). The detection rates tended to increase as the glaucoma stage progressed, and in Stage M3, these were 93.9% and 78.8% for the CG and analog noises, respectively. The PPG eyes did not exhibit subjective abnormalities for both noises. The specificity values were 97.1% and 100% for the CG and analog noises, respectively.

Conclusion

The CG noise is more effective than the analog noise in evaluating the subjective perception of visual field abnormalities in patients with glaucoma.
Quantifying the fitness effects of resistance alleles with and without anthelmintic selection pressure using Caenorhabditis elegans
Authors: Shaver Amanda O. , Miller Isabella R. , Schaye Etta S. , Moya Nicolas D. , Collins J. B. , Wit Janneke , Blanco Alyssa H. , Shao Fiona M. , Andersen Elliot J. , Khan Sharik A. , Paredes Gracie , Andersen Erik C.
Published: May 2024

Albendazole (a benzimidazole) and ivermectin (a macrocyclic lactone) are the two most commonly co-administered anthelmintic drugs in mass-drug administration programs worldwide. Despite emerging resistance, we do not fully understand the mechanisms of resistance to these drugs nor the consequences of delivering them in combination. Albendazole resistance has primarily been attributed to variation in the drug target, a beta-tubulin gene. Ivermectin targets glutamate-gated chloride channels (GluCls), but it is unknown whether GluCl genes are involved in ivermectin resistance in nature. Using Caenorhabditis elegans, we defined the fitness costs associated with loss of the drug target genes singly or in combinations of the genes that encode GluCl subunits. We quantified the loss-of-function effects on three traits: (i) multi-generational competitive fitness, (ii) fecundity, and (iii) development. In competitive fitness and development assays, we found that a deletion of the beta-tubulin gene ben-1 conferred albendazole resistance, but ivermectin resistance required the loss of two GluCl genes (avr-14 and avr-15). The fecundity assays revealed that loss of ben-1 did not provide any fitness benefit in albendazole conditions and that no GluCl deletion mutants were resistant to ivermectin. Next, we searched for evidence of multi-drug resistance across the three traits. Loss of ben-1 did not confer resistance to ivermectin, nor did loss of any single GluCl subunit or combination confer resistance to albendazole. Finally, we assessed the development of 124 C. elegans wild strains across six benzimidazoles and seven macrocyclic lactones to identify evidence of multi-drug resistance between the two drug classes and found a strong phenotypic correlation within a drug class but not across drug classes. Because each gene affects various aspects of nematode physiology, these results suggest that it is necessary to assess multiple fitness traits to evaluate how each gene contributes to anthelmintic resistance.