bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comprehensive transcriptomic analysis and machine learning reveal unique gene expression profiles in patients with immune‐mediated necrotizing myopathy
Authors: Liu Hongjiang , Deng Lin , Guo Yixue , Liu Huan , Chen Bo , Zhang Jiaqian , Ran Jingjing , Yin Geng , Xie Qibing 
Published: September 2023

AbstractBackgroundImmune‐mediated necrotizing myopathy (IMNM) is an autoimmune myopathy characterized by severe proximal weakness and muscle fiber necrosis, yet its pathogenesis remains unclear. So far, there are few bioinformatics studies on underlying pathogenic genes and infiltrating immune cell profiles of IMNM. Therefore, we aimed to characterize differentially expressed genes (DEGs) and infiltrating cells in IMNM muscle biopsy specimens, which may be useful for elucidating the pathogenesis of IMNM.MethodsThree datasets (GSE39454, GSE48280 and GSE128470) of gene expression profiling related to IMNM were obtained from the Gene Expression Omnibus database. Data were normalized, and DEG analysis was performed using the limma package. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses of DEGs were performed using clusterProfiler. The CIBERSORT algorithm was performed to identify infiltrating cells. Machine learning algorithm and gene set enrichment analysis (GSEA) were performed to find distinctive gene signatures and the underlying signaling pathways of IMNM.ResultsDEG analysis identified upregulated and downregulated in IMNM muscle compared to the gene expression levels of other groups. GO and KEGG analysis showed that the pathogenesis of IMNM was notable for the under‐representation of pathways that were important in dermatomyositis and inclusion body myositis. Three immune cells (M2 macrophages, resting dendritic cells and resting natural killer cells) with differential infiltration and five key genes (NDUFAF7, POLR2J, CD99, ARF5 and SKAP2) in patients with IMNM were identified through the CIBERSORT and machine learning algorithm. The GSEA results revealed that the key genes were remarkably enriched in diverse immunological and muscle metabolism‐related pathways.ConclusionsWe comprehensively explored immunological landscape of IMNM, which is indicative for the research of IMNM pathogenesis.
Generative adversarial networks‐based super‐resolution algorithm enables high signal‐to‐noise ratio spatial heterodyne Raman spectra
Authors: Hu Lilei , Shen Jingxuan , Chen Zhu , Zhang Yichen , Chen Chang 
Published: September 2023

AbstractHigh‐resolution interference pattern images are vital for spatial heterodyne Raman spectroscopy to produce quality Raman spectra with a good signal‐to‐noise ratio. A sought‐after super‐resolution algorithm can enhance Raman interference pattern images, reducing reliance on expensive imaging sensors. This enables miniaturization and portability for point‐of‐care testing. This study proposes a generative adversarial network (GAN)‐based super‐resolution reconstruction algorithm explicitly designed for Raman interference patterns. Employing GAN adversarial training, the algorithm effectively reconstructs interference pattern images at higher resolution, improving Raman spectra signal‐to‐noise ratio. Considering Raman spectra analysis mainly focuses on characteristic peaks, a Raman characteristic peak‐focused network training scheme is used. For instance, acetaminophen is studied with two selected Raman characteristic peaks centered at 388 and 858 cm−1. These peaks are observed in Fourier transformed Raman spectra from corresponding low‐resolution interference pattern images obtained by down‐sampling high‐resolution ones by twofold and fourfold. The proposed GAN‐based algorithm successfully reconstructs low‐resolution interference patterns into high‐resolution ones, achieving highR‐square values (96.05% for twofold and 91.1% for fourfold). This innovation holds potential for point‐of‐care applications, like noninvasive blood glucose concentration measurements, enabling cost‐effective, portable Raman spectrometers with improved capabilities.
Riboflavin improves grain yield, 2‐acetyl‐1‐pyrroline accumulation, and antioxidative properties of fragrant rice
Authors: Cheng Siren , Liu Haidong , Li Keqing , Zheng Likai , Su Meilin , Lin Xueer , Huang Guobao , Ren Yong 
Published: September 2023

AbstractBACKGROUNDRiboflavin, a vital water‐soluble vitamin with antioxidative activity, plays a critical role in maintaining overall bodily health and defense responses. However, its impact on fragrant rice yield and aroma remains unexplored.RESULTSIn a 2022 pot experiment with Meixiangzhan and Yuxiangyouzhan fragrant rice cultivars, we applied riboflavin foliar treatments at concentrations of 0 (CK), 10 (R10), 20 (R20), and 40 (R40) mg L−1 during the initial heading stage. Riboflavin increased rice yield, 2‐acetyl‐1‐pyrroline (2‐AP) content, and antioxidative properties. It boosted 2‐AP level by 13.1–50.1% for Meixiangzhan and 22.3–35.3% for Yuxiangyouzhan, with the highest levels in R20 and R10 treatments. This increase is significantly correlated with elevated levels of proline, pyrroline‐5‐carboxylic acid, pyrroline, and methylglyoxal, as well as heightened enzyme activities, including those of proline dehydrogenase, ornithine aminotransferase, and pyrroline‐5‐carboxylic acid synthetase (P5CS). The R20 treatment resulted in the highest yield due to an improved seed‐setting rate. Importantly, a positive correlation emerged between 2‐AP content and yield, both significantly linked to superoxide dismutase, proline, hydrogen peroxide, P5CS, catalase, and pyrroline.CONCLUSIONRiboflavin maintained enzyme activities, regulated substance synthesis pathways, and increased 2‐AP and yield, especially in the R20 treatment. These insights advance fragrant rice production theory by uncovering riboflavin's role in the development of fragrant rice. © 2023 Society of Chemical Industry.
Spatial patterns of soil stoichiometry and their responses to land use in a desertified area: A case study of China's Horqin Sandy Land
Authors: Cao Wenjie , Li Yuqiang , Chen Yun , Chen Yinping , Wang Xuyang 
Published: September 2023

AbstractEcological stoichiometry facilitates the understanding of biogeochemical cycles by studying the balance among multiple elements in ecosystems. However, the spatial patterns of soil stoichiometry and their responses to land use in desertified land are unclear. In this study, we selected 525 sample points to collect topsoil (0–20 cm) samples throughout China's Horqin Sandy Land and measured soil organic carbon (SOC), total nitrogen (TN), and total phosphorus (TP). We then calculated stoichiometric ratios (C:N:P). SOC (8.7 g kg−1), TN (0.9 g kg−1), and TP (0.3 g kg−1) were lower in this region than in Chinese and global terrestrial ecosystems due to aeolian desertification. SOC, TN, C:P, and N:P were significantly (p < 0.05) higher in grassland, followed by woodland, cropland, and sandy land. This sequence may result from the large number of dead roots that participate in the SOC turnover in grassland. TP was significantly higher in cropland due to fertilization. C:N did not differ significantly (p > 0.05) among grassland, woodland, and cropland because of the strong coupling relationship between SOC and TN. The values of SOC, TN, TP, C:P, and N:P in the Horqin Sandy Land were high in the north (dominated by mountain woodland and grassland) and were low in the south (dominated by desertified land). SOC, TN, and TP contents and C:N:P ratios were mainly affected by mean annual temperature (29.6%), land use (11.5%), and bulk density (11.4%) through their influence on soil microbial metabolism, litter and nutrient input, and soil structure, respectively. The results provide information on the overall changes in soil stoichiometry in the Horqin Sandy Land and its responses to land‐use changes, and can therefore guide ecological restoration in semiarid regions affected by desertification in the modern context of climate change.
Research on bidirectional beam tracking and performance analysis of optical communication system with microvibrations
Authors: Teng Yunjie , Qin Hao , Zhang Min 
Published: September 2023

AbstractThe impact of tracking errors over the vibration interference is investigated. A novel expression is presented for the bidirectional laser tracking mechanism which takes in account both periscope communication terminal and beam acquisition process with beaconless technology. In this paper, platform microvibrations are measured and compensated to improve the tracking characteristics of the optical communication terminal. An experiment was conducted to verify the high precision tracking system with the combination of coarse and fine tracking technologies, which represents that the fine tracking error is suppressed to 2.1 μrad. This high precision implementation demonstrates the effectiveness of the tracking control loop, and will contribute to the space laser communication.
National Improvement of Waiting Times: First Results From the Dutch Head and Neck Audit
Authors: van Oorschot Hanneke Doremiek , de Jel Dominique Valérie Clarence , Hardillo Jose Angelito , Smeele Ludi E. , Baatenburg de Jong Robert Jan ,   the Dutch Head and Neck Audit Group
Published: September 2023

AbstractObjectiveTimely treatment initiation in head and neck cancer (HNC) care is of great importance regarding survival, oncological, functional, and psychological outcomes. Therefore, waiting times are assessed in the Dutch Head and Neck Audit (DHNA). This audit aims to assess and improve the quality of care through feedback and benchmarking. For this study, we examined how waiting times evolved since the start of the DHNA.Study DesignProspective cohort study.SettingNational multicentre study.MethodsThe DHNA was established in 2014 and reached national coverage of all patients treated for primary HNC in 2019. DHNA data on curative patients from 2015 to 2021 was extracted on national (benchmark) and hospital level. We determined 3 measures for waiting time: (1) the care pathway interval (CPI, first visit to start treatment), (2) the time to treatment interval (TTI, biopsy to start treatment), and (3) CPI‐/TTI‐indicators (percentage of patients starting treatment ≤30 days). The Dutch national quality norm for the CPI‐indicator is 80%.ResultsThe benchmark median CPI and TTI improved between 2015 and 2021 from 37 to 26 days and 37 to 33 days, respectively. Correspondingly, the CPI‐ and TTI‐indicators, respectively, increased from 39% to 64% and 35% to 40% in 2015 to 2021. Outcomes for all hospitals improved and dispersion between hospitals declined. Four hospitals exceeded the 80% quality norm in 2021.ConclusionWaiting times improved gradually over time, with 4 hospitals exceeding the quality standard in 2021. On the hospital‐level, process improvement plans have been initiated. Systematic registration, auditing, and feedback of data support the improvement of quality of care.
Reducing Pediatric Posttonsillectomy Opioid Prescribing: A Quality Improvement Initiative
Authors: Amin Shaunak N. , Thompson Trey , Wang Xing , Goldklang Samantha , Martin Lynn D. , Low Daniel K.‐W. , Parikh Sanjay R. , Sie Kathleen C. , Dahl John P. 
Published: September 2023

AbstractObjectivePostoperative pain is the most common morbidity associated with tonsillectomy. Opioids are frequently used in multimodal posttonsillectomy analgesia regimens; however, concerns regarding respiratory depression, drug‐drug interactions, and medication misuse necessitate responsible opioid stewardship among prescribing surgeons. It is unclear if intentionally reducing opioid prescription doses negatively affects the patient experience.MethodsA quality improvement team reviewed all posttonsillectomy opioid prescriptions at a pediatric ambulatory surgery center between January and June 2021 (preintervention, 163 patients). Following this review, we performed an opioid education session for surgeons and studied opioid prescribing habits between July and December 2021 (Plan‐Do‐Study‐Act [PDSA] 1, 152 patients). We then implemented a standardized prescription protocol of 7 doses of oxycodone per patient and again reviewed prescriptions between January and June 2022 (PDSA 2, 178 patients). The following measures were evaluated: initial number of opioid doses prescribed, need for refills, 7‐day emergency department (ED) visits, and readmissions.ResultsEach intervention reduced the average number of initial oxycodone doses per patient (12.2 vs 9.2 vs 6.9 doses, P < .001). There were no changes in the rate of refill requests, 7‐day ED visits, and readmissions, by descriptive or Statistical Process Control analyses.DiscussionIn 2 PDSA cycles, we achieved a 43% reduction in the number of doses of oxycodone prescribed following tonsillectomy. We did not observe any increased rates in balancing measures, which are surrogates for unintentional effects of PDSA changes, including refills, ED presentations, and readmission rates.Implications for PracticeDirected provider education and standardized posttonsillectomy prescription protocols can safely decrease postoperative opioid prescribing. Further PDSA cycles are required to consider even fewer opioid prescription doses.
Integrating biocultural conservation and sociocultural valuation in the management of sacred forests: What values are important to the public?
Authors: Ihemezie Eberechukwu Johnpaul , Albaladejo‐García José A. , Stringer Lindsay C. , Dallimer Martin 
Published: September 2023

Abstract

The need to recognise plural values and integrate these into policy design has long been of interest in nature conservation. However, we also need to understand whether and how different values are prioritised among diverse stakeholders. This is particularly important when indigenous and traditional cultures play a role in how land is managed and protected.

Working in the sacred forests of Nigeria, we applied the principles of biocultural conservation and sociocultural valuation to understand the values that underpin people's relationship with nature and with other users of nature. We operationalised this by employing participatory workshop methods to identify multiple values of sacred forests, and conjoint analysis to elicit local people's value priorities and preferences for conserving sacred forests.

We identified multiple values attributed to sacred forests, but the strongest preferences were for improved provision of medicinal values. However, preference heterogeneity analysis showed that sacred forests are valued differently among clusters of people with distinct sociodemographic profiles.

Our findings also showed that the current management strategy for the conservation of sacred forests is inadequate to galvanise shared and collective responsibility from diverse stakeholders. Using a value‐based approach, more robust management strategies that will yield high utility to the public were determined and recommended for implementation.

Policy implications. Overall, our study demonstrates that sacred forests are valued in multiple ways above and beyond their role in a cultural belief system. New strategies are therefore needed to effectively manage and conserve them. We recommend a plural approach to the conservation of sacred forests that will incorporate multiple values. This can be achieved by integrating biocultural conservation and sociocultural valuation.

Read the free Plain Language Summary for this article on the Journal blog.
Iron insertion into coproporphyrin III‐ferrochelatase complex: Evidence for an intermediate distorted catalytic species
Authors: Gabler Thomas , Dali Andrea , Sebastiani Federico , Furtmüller Paul Georg , Becucci Maurizio , Hofbauer Stefan , Smulevich Giulietta 
Published: September 2023

AbstractUnderstanding the reaction mechanism of enzymes at the molecular level is generally a difficult task, since many parameters affect the turnover. Often, due to high reactivity and formation of transient species or intermediates, detailed information on enzymatic catalysis is obtained by means of model substrates. Whenever possible, it is essential to confirm a reaction mechanism based on substrate analogues or model systems by using the physiological substrates. Here we disclose the ferrous iron incorporation mechanism, in solution, and in crystallo, by the coproporphyrin III‐coproporphyrin ferrochelatase complex from the firmicute, pathogen, and antibiotic resistant, Listeria monocytogenes. Coproporphyrin ferrochelatase plays an important physiological role as the metalation represents the penultimate reaction step in the prokaryotic coproporphyrin‐dependent heme biosynthetic pathway, yielding coproheme (ferric coproporphyrin III). By following the metal titration with resonance Raman spectroscopy and x‐ray crystallography, we prove that upon metalation the saddling distortion becomes predominant both in the crystal and in solution. This is a consequence of the readjustment of hydrogen bond interactions of the propionates with the protein scaffold during the enzymatic catalysis. Once the propionates have established the interactions typical of the coproheme complex, the distortion slowly decreases, to reach the almost planar final product.
Evaluating hybrid controls methodology in early‐phase oncology trials: A simulation study based on the MORPHEUS‐UC trial
Authors: Wang Guanbo , Poulin‐Costello Melanie , Pang Herbert , Zhu Jiawen , Helms Hans‐Joachim , Reyes‐Rivera Irmarie , Platt Robert W. , Pang Menglan , Koukounari Artemis 
Published: September 2023

AbstractPhase Ib/II oncology trials, despite their small sample sizes, aim to provide information for optimal internal company decision‐making concerning novel drug development. Hybrid controls (a combination of the current control arm and controls from one or more sources of historical trial data [HTD]) can be used to increase statistical precision. Here we assess combining two sources of Roche HTD to construct a hybrid control in targeted therapy for decision‐making via an extensive simulation study. Our simulations are based on the real data of one of the experimental arms and the control arm of the MORPHEUS‐UC Phase Ib/II study and two Roche HTD for atezolizumab monotherapy. We consider potential complications such as model misspecification, unmeasured confounding, different sample sizes of current treatment groups, and heterogeneity among the three trials. We evaluate two frequentist methods (with both Cox and Weibull accelerated failure time [AFT] models) and three different commensurate priors in Bayesian dynamic borrowing (with a Weibull AFT model), and modifications within each of those, when estimating the effect of treatment on survival outcomes and measures of effect such as marginal hazard ratios. We assess the performance of these methods in different settings and the potential of generalizations to supplement decisions in early‐phase oncology trials. The results show that the proposed joint frequentist methods and noninformative priors within Bayesian dynamic borrowing with no adjustment on covariates are preferred, especially when treatment effects across the three trials are heterogeneous. For generalization of hybrid control methods in such settings, we recommend more simulation studies.
Natural compounds against nonalcoholic fatty liver disease: A review on the involvement of the LKB1/AMPK signaling pathway
Authors: Omidkhoda Navid , Mahdiani Sina , Hayes A. Wallace , Karimi Gholamreza 
Published: September 2023

AbstractAlthough various therapeutic approaches are used to manage nonalcoholic fatty liver disease (NAFLD), the best approach to NAFLD management is unclear. NAFLD is a liver disorder associated with obesity, metabolic syndrome, and diabetes mellitus. NAFLD progression can lead to cirrhosis and end‐stage liver disease. Hepatic kinase B1 (LKB1) is an upstream kinase of 5′‐adenosine monophosphate‐activated protein kinase (AMPK), a crucial regulator in hepatic lipid metabolism. Activation of LKB1/AMPK inhibits fatty acid synthesis, increases mitochondrial β‐oxidation, decreases the expression of genes encoding lipogenic enzymes, improves nonalcoholic steatohepatitis, and suppresses NAFLD progression. One potential opening for new and safe chemicals that can tackle the NAFLD pathogenesis through the LKB1‐AMPK pathway includes natural bioactive compounds. Accordingly, we summarized in vitro and in vivo studies regarding the effect of natural bioactive compounds such as a few members of the polyphenols, terpenoids, alkaloids, and some natural extracts on NAFLD through the LKB1/AMPK signaling pathway. This manuscript may shed light on the way to finding a new therapeutic agent for NAFLD management.
What do the children and teachers say?: Voices on gender stereotyping in children's literature for MalaysianESLclassrooms
Authors: Yeoh Hai Nin , Cheong Huey Fen 
Published: September 2023

AbstractThis preliminary study analyses children's and teachers' views towards gender stereotyping in children's literature for Malaysian ESL (English as a Second Language) classrooms. We employed focus groups with 14 children (aged 10–12) and interviews with 6 experienced ESL teachers, in which children and teachers reflected on selected literature taught in schools. Our findings suggested that both children and teachers overlooked gender stereotyping in the selected children's literature as they focused more on the storyline and moral values. However, our focus groups with children showed their potential in adapting the reading materials to their social context, despite the typical belief that young children blindly learn and accept anything presented to them. Comparison between the boys and girls also showed different gendered responses towards gender stereotyping, with the boys showing stronger support for gender equality. The children insisted that men and women are equals and suggested more active male participation in domestic settings could indicate their readiness to discuss gender‐related issues. In addition, our interviews with teachers led to their call for more reading materials that reflect gender equality. The teachers admitted to a lack of explicit discussions about gender in their current teaching/learning process and expressed their willingness to include gender discussions with their students in the future. This study hopes to give voices to Malaysian children and teachers in the Global South, highlighting their potential for agency in pedagogical review and gender advocacy in education.Context and implicationsRationale for this studyThis study explores children's views' and teachers' strategies for addressing gender stereotyping in children's literature for Malaysian ESL classrooms.Why the new findings matterOur findings highlight the need for training for teachers and teaching/learning materials that reflect gender equality. Our findings signal children's readiness to discuss gender and the importance of teachers' role in fostering such discussions.Implications for practitioners and policy makersThis study is significant for teachers and curriculum reviewers in highlighting how children's literature may influence children and foster gender equality. There is a need for support materials, training for teachers and careful selection of suitable reading materials for children in terms of cultural and gender values.