bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis and identification of oxidative stress-ferroptosis related biomarkers in ischemic stroke
Authors: Zhang Lin-Ming , Liang Xing-ling , Xiong Gui-fei , Xing xuan-lin , Zhang Qiu-juan , Zhang Bing-ran , Liu Ming-wei
Published: February 2024

Studies have shown that a series of molecular events caused by oxidative stress is associated with ferroptosis and oxidation after ischemic stroke (IS). Differential analysis was performed to identify differentially expressed mRNA (DEmRNAs) between IS and control groups. Critical module genes were identified using weighted gene co-expression network analysis (WGCNA). DEmRNAs, critical module genes, oxidative stress-related genes (ORGs), and ferroptosis-related genes (FRGs) were crossed to screen for intersection mRNAs. Candidate mRNAs were screened based on the protein–protein interaction (PPI) network and the MCODE plug-in. Biomarkers were identified based on two types of machine learning algorithms, and the intersection was obtained. Functional items and related pathways of the biomarkers were identified using gene set enrichment analysis (GSEA). Finally, single-sample GSEA (ssGSEA) and Wilcoxon tests were used to identify differential immune cells. An miRNA-mRNA-TF network was created. Quantitative real-time polymerase chain reaction (qRT-PCR) was performed to verify the expression levels of biomarkers in the IS and control groups. There were 8287 DE mRNAs between the IS and control groups. The genes in the turquoise module were selected as critical module genes for IS. Thirty intersecting mRNAs were screened for overlaps. Seventeen candidate mRNAs were also identified. Four biomarkers (CDKN1A, GPX4, PRDX1, and PRDX6) were identified using two types of machine-learning algorithms. GSEA results indicated that the biomarkers were associated with steroid biosynthesis. Nine types of immune cells (activated B cells and neutrophils) were markedly different between the IS and control groups. We identified 3747 miRNA-mRNA-TF regulatory pairs in the miRNA-mRNA-TF regulatory network, including hsa-miR-4469-CDKN1A-BACH2 and hsa-miR-188-3p-GPX4-ATF2. CDKN1A, PRDX1, and PRDX6 were upregulated in IS samples compared with control samples. This study suggests that four biomarkers (CDKN1A, GPX4, PRDX1, and PRDX6) are significantly associated with IS. This study provides a new reference for the diagnosis and treatment of IS.
Structural insights into the ubiquitylation strategy of the oligomeric CRL2FEM1B E3 ubiquitin ligase
Authors: Dai Zonglin , Liang Ling , Wang Weize , Zuo Peng , Yu Shang , Liu Yaqi , Zhao Xuyang , Lu Yishuo , Jin Yan , Zhang Fangting , Ding Dian , Deng Weiwei , Yin Yuxin
Published: February 2024

Cullin-RING E3 ubiquitin ligase (CRL) family members play critical roles in numerous biological processes and diseases including cancer and Alzheimer’s disease. Oligomerization of CRLs has been reported to be crucial for the regulation of their activities. However, the structural basis for its regulation and mechanism of its oligomerization are not fully known. Here, we present cryo-EM structures of oligomeric CRL2FEM1B in its unneddylated state, neddylated state in complex with BEX2 as well as neddylated state in complex with FNIP1/FLCN. These structures reveal that asymmetric dimerization of N8-CRL2FEM1B is critical for the ubiquitylation of BEX2 while FNIP1/FLCN is ubiquitylated by monomeric CRL2FEM1B. Our data present an example of the asymmetric homo-dimerization of CRL. Taken together, this study sheds light on the ubiquitylation strategy of oligomeric CRL2FEM1B according to substrates with different scales.
LET-381/FoxF and its target UNC-30/Pitx2 specify and maintain the molecular identity of C. elegans mesodermal glia that regulate motor behavior
Authors: Stefanakis Nikolaos , Jiang Jessica , Liang Yupu , Shaham Shai
Published: February 2024

While most glial cell types in the central nervous system (CNS) arise from neuroectodermal progenitors, some, like microglia, are mesodermally derived. To understand mesodermal glia development and function, we investigated C. elegans GLR glia, which envelop the brain neuropil and separate it from the circulatory system cavity. Transcriptome analysis shows that GLR glia combine astrocytic and endothelial characteristics, which are relegated to separate cell types in vertebrates. Combined fate acquisition is orchestrated by LET-381/FoxF, a fate-specification/maintenance transcription factor also expressed in glia and endothelia of other animals. Among LET-381/FoxF targets, the UNC-30/Pitx2 transcription factor controls GLR glia morphology and represses alternative mesodermal fates. LET-381 and UNC-30 co-expression in naive cells is sufficient for GLR glia gene expression. GLR glia inactivation by ablation or let-381 mutation disrupts locomotory behavior and promotes salt-induced paralysis, suggesting brain-neuropil activity dysregulation. Our studies uncover mechanisms of mesodermal glia development and show that like neuronal differentiation, glia differentiation requires autoregulatory terminal selector genes that define and maintain the glial fate.
Integrating multiscale and machine learning approaches towards the SAMPL9 log P challenge
Authors: Draper Michael R. , Waterman Asa , Dannatt Jonathan E. , Patel Prajay
Published: February 2024

This work highlights three approaches integrating quantum mechanics, molecular mechanics, and machine learning towards predicting the partition coefficient (log P) as part of the ninth iteration of the SAMPL challenges.
The effects of Lu3+, Gd3+ and Ga3+ substitution on the photoluminescence of Y2.95−x−yLuxGdyAlzGa5−zO12:0.05Ce3+ phosphors for high-power white AC-LEDs
Authors: Wang Senyu , Wang Ming , Qin Xianzhuang , Xu Zusheng , Wang Jingtao , Zhang Shan , Zhang Rui
Published: February 2024

Various yellowish-green persistent phosphors of Y2.95−x−yLuxGdyAl5−zGazO12:0.05Ce3+ (x = 0–1, y = 0–1, z = 1–4) were successfully synthesized by the one-step high-temperature solid-state reaction method in air.
Silver nanoparticle doped laser-induced graphene fabrication methodology affects silver nanoparticle size, distribution, biological and electrochemical properties
Authors: Sharma Chetan Prakash , Gupta Abhishek , Khadka Meghna , Ben-Yoav Hadar , Ronen Avner , Arnusch Christopher J.
Published: February 2024

Three fabrication methods for metal-doped laser-induced graphene (LIG) are compared resulting in stable nanoparticles embedded within LIG. Variable nanoparticle size, distribution, antibacterial and electrochemical properties were observed.
Redox regulation of electrofluorochromic behavior for an AIEgen-doped PVA hydrogel based on a ferrocene derivate
Authors: Zhang Shang , Li Qiuhong , Liu Hao , Li Xueshu , Wang Xuemei , Du Xueqin , Lv Cuiling , Wang Zhaodong , Li Aixiang , Niu Lin
Published: February 2024

The fluorescent molecule FcMe-TPE with aggregation-induced emission properties was synthesized to prepare an EFC hydrogel material with high conductivity. The obtained hydrogel exhibited reversible fluorescent switching behavior on external stimulus.
Oxidative stress induced conformational changes of human serum albumin
Authors: Brahma Debdip , Sarangi Akshay Narayan , Kaushik Rupal , Gupta Amar Nath
Published: February 2024

Oxidative stress, generated by reactive oxygen species (ROS), is responsible for the loss of structure and functionality of proteins and is associated with several aging-related diseases.
Computational study of two-dimensional SnGe2N4 as a promising photocatalyst for the oxygen evolution reaction
Authors: Ain Noor Ul , Kanwal Arooba , Jalil Abdul , Dee Chang-Fu , Zhao Tingkai , Raza Syed Raza Ali , Ahmad Ishaq
Published: February 2024

2D SnGe2N4 as an appealing photocatalyst driving Oxygen Evolution Reaction (OER).
Wavelength-dependent rearrangements of an α-dione chromophore: a chemical pearl in a bis(hypersilyl) oyster
Authors: Glotz Gabriel , Drusgala Manfred , Hamm Florian , Fischer Roland C. , Došlić Nađa , Kelterer Anne-Marie , Gescheidt Georg , Haas Michael
Published: February 2024

Herein the authors report on the synthesis and photochemistry of a symmetric bissilyl-dione. This compound reveals a wavelength dependent and moreover highly selective photochemistry, which is based on the bissilyl substitution of the dione.
Binary Ni–Cu nanocomposite-modified MXene-adorned 3D-nickel foam for effective overall water splitting and supercapacitor applications
Authors: Raveendran Asha , Chandran Mijun , Siddiqui Masoom Raza , Wabaidur Saikh Mohammad , Angaiah Subramania , Dhanusuraman Ragupathy
Published: February 2024

Herein, a multifunctional binary nickel–copper-modified MXene on nickel foam was synthesized and employed as an electrode material for hydrogen evolution reaction (HER), oxygen evolution reaction (OER), overall water splitting and supercapacitors.
Dual‐Mode Encryption for UC‐Secure String OT from Learning with Errors
Authors: Liu Momeng , Hu Yupu , Lai Qiqi , Zhang Shanshan , Jia Huiwen , Gao Wen , Wang Baocang
Published: February 2024

Universal composability (UC) is a primary security flavor for designing oblivious transfer (OT) due to its advantage of arbitrary composition. However, the study of UC‐secure OT over lattices is still far behind compared with constructions over prequantum assumptions. Relying on the learning with errors (LWE) assumption, Quach proposes a dual‐mode encryption scheme (SCN’20) for deriving a two‐round OT whose security is provably UC‐secure in the common reference string (CRS) model. Due to its use of a randomized rounding function proposed by Benhamouda et al. (PKC’18), this OT can only be limited to transmitting single‐bit messages. Therefore, conducting trivial repetitions of Quach’s OT when transmitting multibit strings would be very costly. In this work, we put forward a modified dual‐mode encryption cryptosystem under the decisional LWE assumption, from which we can derive a UC‐secure string OT with both full‐fledged dual‐mode security and better efficiency on transmitting strings. The key technique we adopt is a key reconciliation scheme proposed by Jiang et al. (PKC’20), which is utilized to extend the single‐bit symmetric encryption key (produced by the aforementioned rounding function) to a multibit case. Through a comprehensive performance analysis, we demonstrate that our proposal can indeed strike a balance between security and efficiency.
Exploring the Reactivity of Substituted [(Allyloxy)methyl]phosphonates in Cycloaddition and Coupling Reactions
Authors: Blot Virginie , M’rabet Hédi , Jmai Momtez , Mathé-Allainmat Monique , Efrit Mohamed Lotfi , Dubreuil Didier , Lebreton Jacques
Published: February 2024

This paper describes the versatility of substituted [(allyl­oxy)methyl]phosphonates to open the way to the synthesis of original phosphonated molecules with heterocyclic architectures. In 1,3-dipolar cycloaddition reactions with nitrile oxides, nitrile imines, and nitrones, these [(allyloxy)methyl]phosphonates react as dipolarophiles to give, regioselectively, the corresponding isoxazolines, pyrazolines, and isoxazolidines. Transition-metal-catalyzed reactions, including inter- or intramolecular Heck coupling, provided access to cinnamyl- and indenyl-linked moieties and phosphonated benzo-fused oxacycles, respectively. Additionally, ring-closing metathesis reactions enabled the synthesis of 2,5-dihydrofurans with the phosphonate group at the anomeric position. In this work, 51 novel phosphorylated heterocyclic compounds, which may find significance in the pharmaceutical and agrochemical fields, were prepared.
Sex Differences in Temporal Sleep Patterns, Social Jetlag, and Attention in High School Adolescents
Authors: Diogo Fernanda Mayara Crispim , Bessa Zoelia Camila Moura , Galina Sabinne Danielle , Oliveira Maria Luiza Cruz de , Silva-Júnior Emanuel Linegley Ribeiro da , Valdez Pablo , Azevedo Carolina Virginia Macêdo de
Published: February 2024

Insufficient sleep and irregular sleep hours are common in adolescents, who experience a delayed sleep phase due to biopsychosocial changes associated with puberty, resulting in later sleep times. However, early morning class hours shorten sleep duration on weekdays. This condition is harmful to cognitive performance, which may be accentuated in girls due to a greater sleep need and less resistance to sleep deprivation. In this study, we evaluated sex differences concerning temporal sleep patterns, social jetlag, and attention in high school adolescents attending morning classes. Students (n = 146 - F: 73–16.1 ± 0.8 years; M: 73–16.2 ± 0.9 years) completed a Health and Sleep questionnaire, kept a sleep diary for 10 days, which incorporated a Maldonado Sleepiness Scale, and performed a Continuous Performance Task. Girls went to bed earlier and woke up on weekends, and spent more time in bed at night and in 24 h on weekdays and weekends, while they also had a greater irregularity in wake-up times (p < 0.05). There were no differences between sexes in terms of social jetlag, sleep debt, and sleepiness upon awakening (p > 0.05). Regarding attention, the girls had a longer reaction time in phasic alertness (p < 0.01) and a tendency to have fewer errors in selective attention (p = 0.06). These results persisted when controlled for sleep parameters. Therefore, we suggest that girls have a greater sleep need and less resistance to sleep deprivation, while the differences in attention performance could be due to different strategies, the girls could be making a trade, increasing reaction time in favor of better accuracy, while the boys could be prioritizing a faster response time.
Sleep Quality in CrossFit: A Cross-Sectional Study
Authors: Simoes Gabriela Duarte , Martins Fernanda de Araujo , Capistrano Jr Valden Luis Matos , Loureiro Luiz Lannes , Souza Marcio Leandro Ribeiro de
Published: February 2024

Objective Based on the relationship between sleep and sports performance, the present study aimed to evaluate sleep quality and excessive daytime sleepiness among adult CrossFit (CrossFit, LLC, Santa Cruz, CA, USA) practitioners and to verify possible associations with intestinal health.

Methods This cross-sectional study involved males and females aged ≥ 18 years who had been regularly practicing CrossFit for at least 3 months. This survey used an online questionnaire addressing demographic and socioeconomic data, disease history, dietary characteristics, and questions regarding CrossFit. To assess intestinal health, the ROME IV Consensus Criteria and Bristol Scale were used. The Pittsburgh International Sleep Quality Index (PSQI-BR) and Epworth Sleepiness Scale were used to assess sleep quality.

Results A total of 1,090 people (73.3% females) with a mean age of 31.2 ± 7.5 years were included. Considering the diagnosis of constipation, 36.9% of the patients were classified as constipated, especially females when compared with males (p < 0.001). On the sleepiness scale, 22.4% of the volunteers showed excessive daytime sleepiness, which was also observed more frequently among females (p = 0.013). In the PSQI-BR, 47.4% of participants were classified as having poor sleep quality (poor sleepers). The overall PSQI-BR score was 5.81 ± 2.85, with no difference between males and females (p = 0.360). There was a positive correlation between the PSQI-BR global score and a diagnosis of constipation and excessive daytime sleepiness. There was a negative correlation between the stool type on the Bristol scale and the PSQI-BR global score.

Conclusion The present study demonstrated that sleep quality was poor among CrossFit users, especially females, which can compromise their training performance.
Place branding: is it public policy, or isn’t it?
Authors: Potapovs Mihails
Published: February 2024

This article explores the question of whether place branding should be considered a public policy. While place branding has gained attention in the fields of marketing and related disciplines, its connection to various public policy areas highlights its broader implications. This study aims to provide conceptual clarity on the matter, arguing for the inclusion of place branding within the public policy discourse. The article employs a conceptual framework to assess the alignment of place branding with the key attributes of public policy. A comparative case study of nation branding practices in seven European countries—Estonia, Italy, Latvia, Luxembourg, Portugal, Spain, and Slovakia—is conducted to assess the applicability of the conceptual framework of public policy to studying nation branding. The case study demonstrates the potential of such approach, highlighting gaps and challenges in the current practices of nation branding. The article concludes by discussing the implications of applying the policy approach to place branding and exploring future research opportunities.
Understanding barriers and facilitators to long-term participation needs in children and young people following acquired brain injuries: a qualitative multi-stakeholder study
Authors: Keetley Rachel , Manning Joseph C. , Williams Jane , Bennett Emily , Westlake Meri , Radford Kathryn
Published: February 2024

Background This study focused on exploring the longer-term participation needs of children and young people with acquired brain injury (CYP-ABI) and their families in one region of the UK and identifying the barriers and facilitators of their participation and well-being to inform the development of a behavioural change intervention for clinical implementation. Methods Qualitative interviews were conducted with CYP-ABI and parents. Focus groups were created with health, education, care and charity stakeholders. The International Classification of Functioning, Disability and Health (ICF) and the Behaviour Change Wheel (BCW) were used to map needs, barriers and facilitators. Results A total of 10 CYP/parent dyads (n = 20) and 17 health, education, care and charity stakeholders were included in this study. Unmet participation needs were mapped to the ICF and barriers/facilitators to the BCW. Significant unmet needs impacting CYP-ABI participation and family well-being were found. Barriers spanned ‘Capability’, ‘Opportunity’ and ‘Motivation’, the greatest being knowledge, skills, social influences, environmental context and resources, social identity and emotion. Facilitators included increasing awareness and understanding, supporting parents, long-term access to specialist assessment and rehabilitation, peer support and integrated collaborative pathways. Conclusion The long-term impact of ABI on CYP and families’ participation and well-being were significant, with barriers spanning every sector and level of society. Implementation of collaborative, cross-sector (education, health and social care) accessible and family-centred care pathways is needed to meet the long-term needs of CYP-ABI and their families, ensuring equity of access. Multi-modal, family-centred, needs-led, theory-based interventions should be co-developed with CYP, families and stakeholders to improve the health and well-being outcomes and the lives of CYP-ABI and their families.
Modeling blood metabolite homeostatic levels reduces sample heterogeneity across cohorts
Authors: Liu Danni , Nagana Gowda G. A. , Jiang Zhongli , Alemdjrodo Kangni , Zhang Min , Zhang Dabao , Raftery Daniel
Published: February 2024

Blood metabolite levels are affected by numerous factors, including preanalytical factors such as collection methods and geographical sites. These perturbations have caused deleterious consequences for many metabolomics studies and represent a major challenge in the metabolomics field. It is important to understand these factors and develop models to reduce their perturbations. However, to date, the lack of suitable mathematical models for blood metabolite levels under homeostasis has hindered progress. In this study, we develop quantitative models of blood metabolite levels in healthy adults based on multisite sample cohorts that mimic the current challenge. Five cohorts of samples obtained across four geographically distinct sites were investigated, focusing on approximately 50 metabolites that were quantified using
1
H NMR spectroscopy. More than one-third of the variation in these metabolite profiles is due to cross-cohort variation. A dramatic reduction in the variation of metabolite levels (90%), especially their site-to-site variation (95%), was achieved by modeling each metabolite using demographic and clinical factors and especially other metabolites, as observed in the top principal components. The results also reveal that several metabolites contribute disproportionately to such variation, which could be explained by their association with biological pathways including biosynthesis and degradation. The study demonstrates an intriguing network effect of metabolites that can be utilized to better define homeostatic metabolite levels, which may have implications for improved health monitoring. As an example of the potential utility of the approach, we show that modeling gender-related metabolic differences retains the interesting variance while reducing unwanted (site-related) variance.
Mutations of the circadian clock genes
Cry
,
Per,
or
Bmal1
have different effects on the transcribed and nontranscribed strands of cycling genes
Authors: Yang Yanyan , Wu Gang , Sancar Aziz , Hogenesch John B.
Published: February 2024

One important goal of circadian medicine is to apply time-of-day dosing to improve the efficacy of chemotherapy. However, limited knowledge of how the circadian clock regulates DNA repair presents a challenge to mechanism-based clinical application. We studied time-series genome-wide nucleotide excision repair in liver and kidney of wild type and three different clock mutant genotypes (
Cry1
−/−
Cry2
−/−
,
Per1
−/−
Per2
−/−
, and
Bmal1
−/−
). Rhythmic repair on the nontranscribed strand was lost in all three clock mutants. Conversely, rhythmic repair of hundreds of genes on the transcribed strand (TSs) persisted in the livers of
Cry1
−/−
Cry2
−/−
and
Per1
−/−
Per2
−/−
mice. We identified a tissue-specific, promoter element-driven repair mode on TSs of collagen and angiogenesis genes in the absence of clock activators or repressors. Furthermore, repair on TSs of thousands of genes was altered when the circadian clock is disrupted. These data contribute to a better understanding of the regulatory role of the circadian clock on nucleotide excision repair in mammals and may be invaluable toward the design of time-aware platinum-based interventions in cancer.
Discourse analysis of male and female representatives of selected countries at the United Nations general
debates
Authors: Alshahrani Abdulaziz
Published: February 2024

The aim of this paper was to evaluate gender differences in the language used in United Nations (UN) General
Assembly debates by one male and one female representative each from India, China, the USA, and Indonesia. The critical discourse
analysis (CDA) framework of van Dijk (2015) was used along with the 25 discursive
devices in this framework. The data on frequencies of variables were analysed statistically. No significant differences were
observed between positive comments about oneself, negative comments about others, length of speech (in words), and the various
devices by the gender of the speaker at the 0.05 level of significance. However, gender differences in terms of higher levels for
males than for females were observed for populism (t(6) = 2.354, p = .057), norm expression
(t(6) = 2.171, p = 0.073), and positive comments about oneself
(t(6) = 2.224, p = .068). The correlation coefficients were significant between genders for
positive-self, norm expression, and national self-glorification only. These results could be attributed to the small size of four
male and four female speeches, leading to high values of standard error, which reflects the significance of differences. Also,
there could be overlapping and mixing of gender characteristics in connection with different contexts and occasions due to
emergent identities. These political identities were created in particular situations or contexts, and it was not clear how much
they could be a result of female or male politicians’ styles. This explanation by Sivrić and
Jurčić (2014) seems to be valid for this research as well. Small samples could be a limitation of this study. However,
many other works used even smaller samples. The generalisability of these findings needs to be tested using other similar
studies.
Exploring teachers’ perspectives on the implementation of a translanguaging pedagogy in two superdiverse Viennese
classrooms
Authors: Cataldo-Schwarzl Lena
Published: February 2024

This article discusses the implementation of translanguaging in two superdiverse school classes and their
teachers’ understanding of translanguaging. Translanguaging as a theory and a transformative pedagogy has recently captured
scholars’ interest from all over the globe, but also earned critique for its transformative claims and ongoing expansion of the
term (Jaspers, 2018, p. 2). Through a triangulation of ethnographic fieldnotes and
interviews, analysed with thematic coding and linguistic text analysis, this study shows that the teachers’ translanguaging
pedagogy is strongly characterised by reoccurring elements, such as translation or reading tasks. The data also reveals teachers’
strong beliefs concerning translanguaging and a gap between the terminology of teachers’ everyday experiences and the terminology
used in research, which both turn out to be resistant to change.
Biomechanical imaging biomarker during chemoradiotherapy predicts treatment response in head and neck squamous cell carcinoma
Authors: Fujimoto Koya , Shiinoki Takehiro , Kawazoe Yusuke , Yuasa Yuki , Mukaidani Wataru , Manabe Yuki , Kajima Miki , Tanaka Hidekazu
Published: February 2024

Objective. For response-adapted adaptive radiotherapy (R-ART), promising biomarkers are needed to predict post-radiotherapy (post-RT) responses using routine clinical information obtained during RT. In this study, a patient-specific biomechanical model (BM) of the head and neck squamous cell carcinoma (HNSCC) was proposed using the pre-RT maximum standardized uptake value (SUVmax) of 18F-fluorodeoxyglucose (FDG) and tumor structural changes during RT as evaluated using computed tomography (CT). In addition, we evaluated the predictive performance of BM-driven imaging biomarkers for the treatment response of patients with HNSCC who underwent concurrent chemoradiotherapy (CCRT). Approach. Patients with histologically confirmed HNSCC treated with definitive CCRT were enrolled in this study. All patients underwent CT two times as follows: before the start of RT (pre-RT) and 3 weeks after the start of RT (mid-RT). Among these patients, 67 patients who underwent positron emission tomography/CT during the pre-RT period were included in the final analysis. The locoregional control (LC), progression-free survival (PFS), and overall survival (OS) prediction performances of whole tumor stress change (TS) between pre- and mid-RT computed using BM were assessed using univariate, multivariate, and Kaplan–Meier survival curve analyses, respectively. Furthermore, performance was compared with the pre and post-RT SUVmax, tumor volume reduction rate (TVRR) during RT, and other clinical prognostic factors. Main results. For both univariate, multivariate, and survival curve analyses, the significant prognostic factors were as follows (p < 0.05): TS and TVRR for LC; TS and pre-RT FDG-SUVmax for PFS; and TS only for OS. In addition, for 2 year LC, PFS, and OS prediction, TS showed a comparable predictive performance to post-RT FDG-SUVmax. Significance. BM-driven TS is an effective prognostic factor for tumor treatment response after CCRT. The proposed method can be a feasible functional imaging biomarker that can be acquired during RT using only routine clinical data and may provide useful information for decision-making during R-ART.
Self-supervised dual-domain balanced dropblock-network for low-dose CT denoising
Authors: An Ran , Chen Ke , Li Hongwei
Published: February 2024

Objective. Self-supervised learning methods have been successfully applied for low-dose computed tomography (LDCT) denoising, with the advantage of not requiring labeled data. Conventional self-supervised methods operate only in the image domain, ignoring valuable priors in the sinogram domain. Recently proposed dual-domain methods address this limitation but encounter issues with blurring artifacts in the reconstructed image due to the inhomogeneous distribution of noise levels in low-dose sinograms. Approach. To tackle this challenge, this paper proposes SDBDNet, an end-to-end dual-domain self-supervised method for LDCT denoising. With the network designed based on the properties of inhomogeneous noise in low-dose sinograms and the principle of moderate sinogram-domain denoising, SDBDNet achieves effective denoising in dual domains without introducing blurring artifacts. Specifically, we split the sinogram into two subsets based on the positions of detector cells to generate paired training data with high similarity and independent noise. These sub-sinograms are then restored to their original size using 1D interpolation and learning-based correction. To achieve adaptive and moderate smoothing in the sinogram domain, we integrate Dropblock, a type of convolution layer with regularization, into SDBDNet, and set a weighted average between the denoised sinograms and their noisy counterparts, leading to a well-balanced dual-domain approach. Main results. Numerical experiments show that our method outperforms popular non-learning and self-supervised learning methods, demonstrating its effectiveness and superior performance. Significance. While introducing a novel high-performance dual-domain self-supervised LDCT denoising method, this paper also emphasizes and verifies the importance of appropriate sinogram-domain denoising in dual-domain methods, which might inspire future work.
Country-level methane emissions and their sectoral trends during 2009–2020 estimated by high-resolution inversion of GOSAT and surface observations
Authors: Janardanan Rajesh , Maksyutov Shamil , Wang Fenjuan , Nayagam Lorna , Sahu Saroj Kumar , Mangaraj Poonam , Saunois Marielle , Lan Xin , Matsunaga Tsuneo
Published: February 2024

Considering the significant role of global methane emissions in the Earth’s radiative budget, global or regionally persistent increasing trends in its emission are of great concern. Understanding the regional contributions of various emissions sectors to the growth rate thus has policy relevance. We used a high-resolution global methane inverse model to independently optimize sectoral emissions using GOSAT and ground-based observations for 2009–2020. Annual emission trends were calculated for top-emitting countries, and the sectoral contributions to the total anthropogenic trend were studied. Global total posterior emissions show a growth rate of 2.6 Tg yr−2 (p < 0.05), with significant contributions from waste (1.1 Tg yr−2) and agriculture (0.9 Tg yr−2). Country-level aggregated sectoral emissions showed statistically significant (p < 0.1) trends in total posterior emissions for China (0.56 Tg yr−2), India (0.22 Tg yr−2), United States (0.65 Tg yr−2), Pakistan (0.22 Tg yr−2) and Indonesia (0.28 Tg yr−2) among the top methane emitters. Emission sectors contributing to the above country-level emission trend are, China (waste 0.35; oil and gas 0.07 Tg yr−2), India (agriculture 0.09; waste 0.11 Tg yr−2), United States (oil and gas 1.0; agriculture 0.07; coal −0.15 Tg yr−2), Brazil (waste 0.09; agriculture 0.08 Tg yr−2), Russia (waste 0.04; biomass burning 0.15; coal 0.11; oil and gas −0.42 Tg yr−2), Indonesia (coal 0.28 Tg yr−2), Canada (oil and gas 0.08 Tg yr−2), Pakistan (agriculture 0.15; waste 0.03 Tg yr−2) and Mexico (waste 0.04 Tg yr−2). Additionally, our analysis showed that methane emissions from wetlands in Russia (0.24 Tg yr−2) and central African countries such as Congo (0.09 Tg yr−2), etc. have a positive trend with a considerably large increase after 2017, whereas Bolivia (−0.09 Tg yr−2) have a declining trend. Our results reveal some key emission sectors to be targeted on a national level for designing methane emission mitigation efforts.
Effect of electron–phonon interactions on a three-level QD-based spaser: linear and quadratic potentials
Authors: Purohit Ankit , Poonia Vishvendra Singh , Mishra Akhilesh Kumar
Published: February 2024

In this article, we study the effect of electron–phonon interaction on a spaser (surface plasmon amplification by stimulated emission of radiation) system consisting of a metal nanoparticle surrounded by a large number of quantum dots (QDs). Usually, the effect of electron–phonon interaction is neglected in the spaser-related literature. However, gain media, in this case QDs, attributed by the large Raman scattering cross-section, exhibit stronger electron–phonon interaction. In the present work, we investigate the effects of electron–phonon interaction on a three-level QD-based spaser. We consider two types of interaction potentials, linear and quadratic, and analyse their effects individually. First, we focus on the linear electron–phonon interaction that perturbs the electrons present in the excited state. This yields a periodic steady-state number of localized surface plasmons (LSPs). The accompanying analytic solution reveals that the population inversion of the gain medium depends on the linear potential strength (Frohlich constant) but does not affect the threshold of spaser considerably for the given numerical parameters. In addition to the LSP, phonons are generated during this process, the temporal dynamics of which are also presented here. Initially, the number of phonons exhibit decaying periodic oscillations, whose amplitude depends on the strength of the electron–phonon interaction. Under continuous pumping, at later times, the number of phonons reaches a steady-state value, which may find potential applications in the realization of continuous phonon nanolasers. Furthermore, the effect of the quadratic potential is investigated phenomenologically by increasing the excited-state decay rate. This results in numerous LSPs and an intense spaser spectrum.
Efficient mitosis detection: leveraging pre-trained faster R-CNN and cell-level classification
Authors: R Shihabuddin Abdul , Beevi K Sabeena
Published: February 2024

The assessment of mitotic activity is an integral part of the comprehensive evaluation of breast cancer pathology. Understanding the level of tumor dissemination is essential for assessing the severity of the malignancy and guiding appropriate treatment strategies. A pathologist must manually perform the intricate and time-consuming task of counting mitoses by examining biopsy slices stained with Hematoxylin and Eosin (H&E) under a microscope. Mitotic cells can be challenging to distinguish in H&E-stained sections due to limited available datasets and similarities among mitotic and non-mitotic cells. Computer-assisted mitosis detection approaches have simplified the whole procedure by selecting, detecting, and labeling mitotic cells. Traditional detection strategies rely on image processing techniques that apply custom criteria to distinguish between different aspects of an image. Additionally, the automatic feature extraction from histopathology images that exhibit mitosis using neural networks.Additionally, the possibility of automatically extracting features from histopathological images using deep neural networks was investigated. This study examines mitosis detection as an object detection problem using multiple neural networks. From a medical standpoint, mitosis at the tissue level was also investigated utilising pre-trained Faster R-CNN and raw image data. Experiments were done on the MITOS-ATYPIA- 14 dataset and TUPAC16 dataset, and the results were compared to those of other methods described in the literature.
Left ventricle segment-specific motion assessment for cardiac-gated radiosurgery
Authors: Poon Justin , Thompson Richard B , Deyell Marc W , Schellenberg Devin , Kohli Kirpal , Thomas Steven
Published: February 2024

Purpose. Cardiac radiosurgery is a non-invasive treatment modality for ventricular tachycardia, where a linear accelerator is used to irradiate the arrhythmogenic region within the heart. In this work, cardiac magnetic resonance (CMR) cine images were used to quantify left ventricle (LV) segment-specific motion during the cardiac cycle and to assess potential advantages of cardiac-gated radiosurgery. Methods. CMR breath-hold cine images and LV contour points were analyzed for 50 controls and 50 heart failure patients with reduced ejection fraction (HFrEF, EF < 40%). Contour points were divided into anatomic segments according to the 17-segment model, and each segment was treated as a hypothetical treatment target. The optimum treatment window (one fifth of the cardiac cycle) was determined where segment centroid motion was minimal, then the maximum centroid displacement and treatment area were determined for the full cardiac cycle and for the treatment window. Mean centroid displacement and treatment area reductions with cardiac gating were determined for each of the 17 segments. Results. Full motion segment centroid displacements ranged between 6–14 mm (controls) and 4–11 mm (HFrEF). Full motion treatment areas ranged between 129–715 mm2 (controls) and 149–766 mm2 (HFrEF). With gating, centroid displacements were reduced to 1 mm (controls and HFrEF), while treatment areas were reduced to 62–349 mm2 (controls) and 83–393 mm2 (HFrEF). Relative treatment area reduction ranged between 38%–53% (controls) and 26%–48% (HFrEF). Conclusion. This data demonstrates that cardiac cycle motion is an important component of overall target motion and varies depending on the anatomic cardiac segment. Accounting for cardiac cycle motion, through cardiac gating, has the potential to significantly reduce treatment volumes for cardiac radiosurgery.
Efficient similar waveform search using short binary codes obtained through a deep hashing technique
Authors: Naoi Makoto , Hirano Shiro
Published: February 2024

A similar waveform search plays a crucial role in seismology for detecting seismic events, such as small earthquakes and low-frequency events. However, the high computational costs associated with waveform cross-correlation calculations represent bottlenecks during the analysis of long, continuous records obtained from numerous stations. In this study, we developed a deep-learning network to obtain 64-bit hash codes containing information on seismic waveforms. Using this network, we performed a similar waveform search for ∼35 million moving windows developed for the 30 min waveforms recorded continuously at 10 MHz sampling rates using 16 acoustic emission transducers during a laboratory hydraulic fracturing experiment. The sampling points of each channel corresponded to those of the 5.8-yr records obtained from typical seismic observations at 100 Hz sampling rates. Of the 35 million windows, we searched for windows with small average Hamming distances among the hash codes of 16 channel waveforms against template hash codes of 6057 events that were catalogued using conventional autoprocessing techniques. The calculation of average Hamming distances is 1430–1530 times faster than that of the corresponding network correlation. This hashing-based template matching enabled the detection of 23 462 additional events. We also demonstrated the feasibility of the hashing-based autocorrelation analysis, where similar event pairs were extracted without templates, by calculating the average Hamming distances for all possible pairs of the ∼35 million windows. This calculation required only 15.5 h under 120 thread parallelization. This deep hashing approach significantly reduced the required memory compared with locality-sensitive hashing approaches based on random permutations, enabling similar waveform searching on a large-scale data set.
Distancing through peacekeeping: global peacekeeping assemblages and the Gambian armed forces
Authors: Dwyer Maggie
Published: February 2024

This article contributes to the understanding of incentives for peacekeeping contribution from non-democratic countries through the largely unexplored case of peacekeeping under authoritarian rule in The Gambia. It argues that President Yahya Jammeh (1994–2017) aimed to use peacekeeping to help keep himself in power, fitting a broader global pattern of peacekeeping for regime maintenance. However, the research also demonstrates that leadership's aims for peacekeeping can be misaligned with the experiences of soldiers. Rather than draw soldiers closer to the regime, the peacekeeping experience involved a distancing from the forces for Gambian soldiers when they returned home. The findings draw on interviews with returned peacekeepers and military decision makers in The Gambia, as well as publications from the armed forces and new public sources of information made available after the 2017 political transition. The article proposes that viewing the deployment experience as a global peacekeeping assemblage helps to understand the more subtle, yet significant, ways in which soldiers' views can shift following peacekeeping deployments.
Brief Communication: The Predictable Network Topology of Evolutionary Genomic Constraint
Authors: Wollenberg Valero Katharina C
Published: February 2024

Large-scale comparative genomics studies offer valuable resources for understanding both functional and evolutionary rate constraints. It is suggested that constraint aligns with the topology of genomic networks, increasing toward the center, with intermediate nodes combining relaxed constraint with higher contributions to the phenotype due to pleiotropy. However, this pattern has yet to be demonstrated in vertebrates. This study shows that constraint intensifies toward the network's center in placental mammals. Genes with rate changes associated with emergence of hibernation cluster mostly toward intermediate positions, with higher constraint in faster-evolving genes, which is indicative of a “sweet spot” for adaptation. If this trend holds universally, network node metrics could predict high-constraint regions even in clades lacking empirical constraint data.
Well-Being Therapy in systemic sclerosis outpatients: a randomized controlled trial
Authors: Romanazzo Sara , Ceccatelli Sara , Mansueto Giovanni , Sera Francesco , Guiducci Serena , Matucci Cerinic Marco , Cosci Fiammetta
Published: February 2024

Objectives

Systemic sclerosis (SSc) patients have psychological distress and poor well-being and need a tailored treatment. Psychological interventions, rarely tested for efficacy, showed poor benefits. The present randomized controlled trial tested the efficacy of Well-Being Therapy (WBT) in SSc patients.

Methods

Thirty-two outpatients were randomized (1:1) to WBT (n = 16) or Treatment As Usual (i.e. routine medical check-ups) (TAU) (n = 16). Primary outcome was well-being. Secondary outcomes included functional ability related to SSc, psychological distress, mental pain, suffering. All participants were assessed at baseline (T0). The WBT group was assessed after two months (end of WBT session 4) (T1), after four months (end of WBT session 8) (T2), after seven months (3-month follow-up) (T3) and after 10 months (6-month follow-up) (T4). The TAU group was assessed two (T1), four (T2), seven (T3) and ten (T4) months after baseline.

Results

WBT produced a significant improvement in subjective well-being (P ≤ 0.001), personal growth (P = 0.006), self-acceptance (P = 0.003) compared with TAU, maintained at T3 as what concerns subjective well-being (P = 0.012). WBT produced a greater decrease in psychological distress (P = 0.010), mental pain (P = 0.010), suffering (P ≤ 0.001) compared with TAU, maintained at T4 as what concerns suffering (P ≤ 0.001). Participants reported high satisfaction with WBT.

Conclusion

The study provides preliminary evidence on the benefits of WBT as short-term approach for in- and out-patient SSc healthcare paths. Studies with larger samples are needed to have the evidence for recommending WBT to SSc patients.
Safety and Efficacy of Bone Marrow and Adipose Tissue-Derived Mesenchymal Stem Cells for the Treatment of Ischemic Stroke: A Systematic Review
Authors: Afshar Hezarkhani Leila , Veysi Kazhal , Rahmani Adibeh , Salari Nader , Hasheminezhad Razie , Nasr Vahideh , Mohammadi Masoud
Published: February 2024

Neurological diseases, including ischemic stroke, are considered a big challenge for public health due to their high prevalence and lack of definitive and effective treatments. Addressing these issues requires innovative therapeutic approaches and among the limited methods available, stem cells have shown promise in improving central nervous system repair by enhancing myelin regeneration and neuronal recovery. To advance this field of research, this systematic review aims to assess the safety and effectiveness of mesenchymal stem cells (MSCs) derived from both bone marrow and adipose tissue for the treatment of ischemic stroke. This study conducted a systematic review in the electronic databases PubMed, Scopus, Web of Science, Embase, ScienceDirect, and Google Scholar to assess the efficacy and safety of MSCs generated from bone marrow and adipose tissue for the treatment of ischemic stroke. It was extracted without a time limit until April 2023. The studies were then transferred to the information management program (EndNote) and duplicates were eliminated. The remaining studies were then examined using the entry and exit criteria and the 3 stages of primary, secondary, and qualitative evaluation, and finally, the results of the final studies were extracted. According to the initial search in the desired databases, 1028 possible related articles were identified and transferred to the information management software (EndNote). After removing 390 duplicate studies, 608 studies were excluded based on inclusion and exclusion criteria. Finally, 37 final studies were included in the systematic review process. Based on the investigations, it was evident that the administration of MSCs derived from both bone marrow and adipose tissue holds significant promise as an effective and safe treatment approach for ischemic stroke. The results consistently showed acceptable outcomes in the studies and this evidence can be recommended for the clinical application of this treatment. Also, the findings of this study report that the use of adipose tissue and bone marrow MSCs in the treatment of ischemic stroke can be used as a practical method.