bluuebunny/crossref_metadata_2025 huggingface dataset:
What do we know about the function of SARS-CoV-2 proteins?
Authors: Justo Arevalo Santiago , Castillo-Chávez Adriana , Uribe Calampa Carmen Sofia , Zapata Sifuentes Daniela , Huallpa César J. , Landa Bianchi Gianfranco , Garavito-Salini Casas Romina , Quiñones Aguilar Mauro , Pineda Chavarría Roberto
Published: September 2023

The COVID-19 pandemic has highlighted the importance in the understanding of the biology of SARS-CoV-2. After more than two years since the first report of COVID-19, it remains crucial to continue studying how SARS-CoV-2 proteins interact with the host metabolism to cause COVID-19. In this review, we summarize the findings regarding the functions of the 16 non-structural, 6 accessory and 4 structural SARS-CoV-2 proteins. We place less emphasis on the spike protein, which has been the subject of several recent reviews. Furthermore, comprehensive reviews about COVID-19 therapeutic have been also published. Therefore, we do not delve into details on these topics; instead we direct the readers to those other reviews. To avoid confusions with what we know about proteins from other coronaviruses, we exclusively report findings that have been experimentally confirmed in SARS-CoV-2. We have identified host mechanisms that appear to be the primary targets of SARS-CoV-2 proteins, including gene expression and immune response pathways such as ribosome translation, JAK/STAT, RIG-1/MDA5 and NF-kβ pathways. Additionally, we emphasize the multiple functions exhibited by SARS-CoV-2 proteins, along with the limited information available for some of these proteins. Our aim with this review is to assist researchers and contribute to the ongoing comprehension of SARS-CoV-2’s pathogenesis.
Isotopic niches of juvenile and adult green turtles (Chelonia mydas) in feeding and nesting areas in Brazil, southwestern Atlantic Ocean
Authors: Fernandes Amanda , Bugoni Leandro , Bianchini Adalto , Zapelini Cleverson , Schiavetti Alexandre
Published: September 2023

Stable isotope analysis is an approach that allows inferring feeding ecology and trophic structure of populations, especially for species that are difficult to observe in natural habitats, such as marine turtles. This study investigated the niche breadth of adult and juvenile green sea turtles (Chelonia mydas) through δ15N and δ13C values in carapace scutes. During 2017 and 2018, tissues were collected from juveniles in a feeding area in southeastern Brazil (n = 60) and from adults in a nesting area in northeastern Brazil, at Fernando de Noronha (n = 21). Our results revealed no temporal variations in the isotopic values of adult green turtles and the mean δ15N values are compatible with the isotopic values of primarily herbivorous animals. In southeastern Brazil, the δ13C values and isotopic niche breadth differences observed in juvenile green turtles suggest that variations in habitat (i.e., channel between the municipalities of Ilhabela and São Sebastião - “SSC” and region comprising the other two municipalities of Ubatuba and Caraguatatuba - “CAU”, as defined in this study based on oceanographic current dynamics) can influence their isotopic niche. The isotopic values observed in juvenile green turtles demonstrated a high degree of feeding behavior plasticity and individual variability, which were possibly influenced by the dynamic of oceanographic currents and seasonal nutrient inputs. These findings help to elucidate the feeding behavior of green turtles at different life stages and the potential influence of oceanographic current dynamics in key feeding sites for juvenile green turtles.
Reconstruction of daily chlorophyll-a concentrations in the transit of severe tropical cyclone Hudhud using the ExDINEOF method
Authors: Wang Zheng , Qiu Shike , Zeng Qun , Du Peijun , Dang Xiaoyan , Liu Jiping , Du Jun
Published: September 2023

Tropical regions experience a diverse range of dense clouds, posing challenges for the daily reconstruction of chlorophyll-a concentration data. This underscores the pressing need for a practical method to reconstruct daily-scale chlorophyll-a concentrations in such regions. While traditional data reconstruction methods focus on single variables and rely on specific factors to infer missing data at specific locations, these single-variable methods may falter when applied to tropical oceans due to the scarcity of available data. Fortunately, all oceanographic variables undergo similar atmospheric and marine dynamic processes, creating internal relationships between them. This allows for the reconstruction of missing data through correlations between variables. Thus, this study introduces a multivariate reconstruction approach using the extended data interpolating empirical orthogonal function (ExDINEOF) method to reconstruct missing daily-scale chlorophyll-a concentration data. The ExDINEOF method considers the simultaneous relationships among multiple variables for data reconstruction in tropical oceans. To verify the method’s robustness, missing data were reconstructed during the formation and passage of severe tropical cyclone Hudhud through the Bay of Bengal. The results demonstrate that ExDINEOF outperforms traditional data reconstruction methods, exhibiting favorable spatial distribution and enhanced accuracy within the dynamic tropical marine environment. Furthermore, an assessment of marine physical environmental factors associated with chlorophyll-a concentration data provides additional evidence for the ExDINEOF method’s accuracy. Notably, the ExDINEOF method offers comprehensive spatial distribution aligned with underlying physical mechanisms governing phytoplankton distribution patterns, detailed phytoplankton growth, bloom, extinction variations in time series, satisfactory accuracy, and comprehensive local-level details.
Association of Wilms tumor-1 protein in urinary exosomes with kidney injury: a population-based cross-sectional study
Authors: Khandpur Sukhanshi , Srivastava Medha , Sharma Rajni , Asif Shafaque , Bhadauria Dharmendra S. , Mishra Prabhaker , Purty Anil J. , Tiwari Swasti
Published: September 2023

Objective

Loss of Wilms tumor-1 (WT1) protein, a podocytopathy marker, through urine exosome (uE), could be an early indication of kidney injury. We examined WT1 in uE (uE-WT1), along with other urine markers of glomerular and kidney tubule injury, in individuals without chronic kidney disease (CKD).

Methodology

The cross-sectional study included individuals who reported having no evidence of chronic kidney disease (CKD). Albumin-to-creatinine ratio (ACR) and estimated glomerular filtration rate (eGFR) were used to assess kidney function. eGFR was calculated using the 2009 CKD-EPI (CKD-Epidemiological) equation. WT1 was analyzed in uE from humans and Wistar rats (before and after the 9th week of diabetes, n = 20). uE-WT1, urinary neutrophil gelatinase-associated lipocalin (NGAL), and kidney injury molecule-1 (KIM-1) were estimated using ELISA. The Kruskal-Wallis H test, Mann-Whitney U test, and stepwise multivariable linear regression were performed.

Results

Urine NGAL and ACR increase with uE-WT1 quartiles (n = 146/quarter). Similarly, uE-WT1, KIM-1, and NGAL were positively associated with ACR. Furthermore, KIM-1, NGAL, and uE-WT1 correlated with ACR. uE-WT1 outperformed KMI-1 and NGAL to explain ACR variability (25% vs. 6% or 9%, respectively). Kidney injury in streptozotocin-induced diabetic rats was associated with a significant rise in uE-WT1. Moreover, the findings were confirmed by the histopathology of kidney tissues from rats.

Conclusion

uE-WT1 was strongly associated with kidney function in rats. In individuals without CKD, uE-WT1 outperformed NGAL as a determinant of differences in ACR.
Renal involvement in eosinophilic granulomatosis with polyangiitis
Authors: Reggiani Francesco , L’Imperio Vincenzo , Calatroni Marta , Pagni Fabio , Sinico Renato Alberto
Published: September 2023

Eosinophilic granulomatosis with polyangiitis (EGPA) is a necrotizing vasculitis, which typically affects small-to medium-sized blood vessels. It is characterized by the presence of tissue infiltrates rich in eosinophils, along with the formation of granulomatous lesions. About 40% of cases have positive anti-neutrophil cytoplasm antibodies (ANCA), with predominant perinuclear staining, and anti-myeloperoxidase (anti-MPO) specificity in about 65% of cases. Typical manifestations of EGPA include the late onset of asthma, nasal and sinus-related symptoms, peripheral neuropathy, and significant eosinophilia observed in the peripheral blood. In contrast to granulomatosis with polyangiitis and microscopic polyangiitis, renal involvement in EGPA is less frequent (about 25%) and poorly studied. Necrotizing pauci-immune crescentic glomerulonephritis is the most common renal presentation in patients with ANCA-positive EGPA. Although rarely, other forms of renal involvement may also be observed, such as eosinophilic interstitial nephritis, mesangial glomerulonephritis, membranous nephropathy, or focal sclerosis. A standardized treatment for EGPA with renal involvement has not been defined, however the survival and the renal outcomes are usually better than in the other ANCA-associated vasculitides. Nonetheless, kidney disease is an adverse prognostic factor for EGPA patients. Larger studies are required to better describe the renal involvement, in particular for patterns different from crescentic glomerulonephritis, and to favor the development of a consensual therapeutic approach. In this article, in addition to personal data, we will review recent findings on patient clinical phenotypes based on ANCA, genetics and the impact of biological drugs on disease management.
Impact of feeding dried distillers’ grains with solubles diet on microbiome and metabolome of ruminal and cecal contents in Guanling yellow cattle
Authors: Song Chun , Zhang Tiantian , Xu Duhan , Zhu Mingming , Mei Shihui , Zhou Bijun , Wang Kaigong , Chen Chao , Zhu Erpeng , Cheng Zhentao
Published: September 2023

Dried distillers’ grains with solubles (DDGS) are rich in nutrients, and partially alternative feeding of DDGS effectively reduces cost of feed and improves animals’ growth. We used 16S rDNA gene sequencing and LC/MS-based metabolomics to explore the effect of feeding cattle with a basal diet (BD) and a Jiang-flavor DDGS diet (replaces 25% concentrate of the diet) on microbiome and metabolome of ruminal and cecal contents in Guanling yellow cattle. The results showed that the ruminal and cecal contents shared the same dominance of Bacteroidetes, Firmicutes and Proteobacteria in two groups. The ruminal dominant genera were Prevotella_1, Rikenellaceae_RC9_gut_group, and Ruminococcaceae_UCG-010; and the cecal dominant genera were Ruminococcaceae_UCG-005, Ruminococcaceae_UCG-010, and Rikenellaceae_RC9_gut_group. Linear discriminant analysis effect size analysis (LDA > 2, P < 0.05) revealed the significantly differential bacteria enriched in the DDGS group, including Ruminococcaceae_UCG_012, Prevotellaceae_UCG_004 and Anaerococcus in the ruminal contents, which was associated with degradation of plant polysaccharides. Besides, Anaerosporobacter, Anaerovibrio, and Caproiciproducens in the cecal contents were involved in fatty acid metabolism. Compared with the BD group, 20 significantly different metabolites obtained in the ruminal contents of DDGS group were down-regulated (P < 0.05), and based on them, 4 significantly different metabolic pathways (P < 0.05) were enriched including “Linoleic acid metabolism,” “Biosynthesis of unsaturated fatty acids,” “Taste transduction,” and “Carbohydrate digestion and absorption.” There were 65 significantly different metabolites (47 were upregulated, 18 were downregulated) in the cecal contents of DDGS group when compared with the BD group, and 4 significantly different metabolic pathways (P < 0.05) were enriched including “Longevity regulating pathway,” “Bile secretion,” “Choline metabolism in cancer,” and “HIF-1 signaling pathway.” Spearman analysis revealed close negative relationships between the top 20 significantly differential metabolites and Anaerococcus in the ruminal contents. Bacteria with high relevance to cecal differential metabolites were Erysipelotrichaceae_UCG-003, Dielma, and Solobacterium that affect specific metabolic pathways in cattle. Collectively, our results suggest that feeding cattle with a DDGS diet improves the microbial structure and the metabolic patterns of lipids and carbohydrates, thus contributing to the utilization efficiency of nutrients and physical health to some extent. Our findings will provide scientific reference for the utilization of DDGS as feed in cattle industry.
Dietary supplementation with Dendrobium officinale leaves improves growth, antioxidant status, immune function, and gut health in broilers
Authors: Zhao Wanqiu , Chen Yue , Tian Yong , Wang Yunzhu , Du Jianke , Ye Xuan , Lu Lizhi , Sun Chongbo
Published: September 2023

Background

TheDendrobium officinaleleaves (DOL) is an underutilized by-product with a large biomass, which have been shown to exhibit immunomodulatory and antioxidant functions. The purpose of this research was to investigate the effects of DOL on broiler growth performance, antioxidant status, immune function, and gut health.

Methods

One hundred and ninety-two 1-day-old chicks were selected and divided into 4 groups at random, 6 replicates for each group and 8 in each. Chicks were given a basal diet supplemented with different amounts of DOL: 0% (control group, NC), 1% (LD), 5% (MD), or 10% (HD). During the feeding trial (70 days), broiler body weight, feed intake, and residual feeding were recorded. On d 70, 12 broilers from each group were sampled for serum antioxidant and immune indexes measurement, intestinal morphological analysis, as well as 16S rRNA sequencing of cecal contents and short-chain fatty acid (SCFA) determination.

Results

In comparison to the NC group, the LD group had greater final body weight and average daily gain, and a lower feed conversion ratio (p< 0.05, d 1 to 70). However, in MD group, no significant change of growth performance occurred (p> 0.05). Furthermore, DOL supplementation significantly improved the levels of serum total antioxidant capacity, glutathione peroxidase, superoxide dismutase, and catalase, but reduced the level of malondialdehyde (p< 0.05). Higher serum immunoglobulin A (IgA) content and lower cytokine interleukin-2 (IL-2) and IL-6 contents were observed in DOL-fed broilers than in control chickens (p<0.05). Compared to the NC group, duodenal villus height (VH) and villus height-to-crypt depth (VH:CD) ratio were considerably higher in three DOL supplementation groups (p< 0.05). Further, 16S rRNA sequencing analysis revealed that DOL increased the diversity and the relative abundance of cecal bacteria, particularly helpful microbes likeFaecalibacterium,Lactobacillus, andOscillospira, which improved the production of SCFA in cecal content. According to Spearman correlation analysis, the increased butyric acid and acetic acid concentrations were positively related to serum antioxidant enzyme activities (T-AOC and GSH-Px) and immunoglobulin M (IgM) level (p< 0.05).

Conclusion

Overall, the current study demonstrated that supplementing the dies with DOL in appropriate doses could enhance growth performance, antioxidant capacity, and immune response, as well as gut health by promoting intestinal integrity and modulating the cecal microbiota in broilers. Our research may serve as a preliminary foundation for the future development and application of DOL as feed additive in broiler chicken diets.
Improved computational epitope profiling using structural models identifies a broader diversity of antibodies that bind to the same epitope
Authors: Spoendlin Fabian C. , Abanades Brennan , Raybould Matthew I. J. , Wong Wing Ki , Georges Guy , Deane Charlotte M.
Published: September 2023

The function of an antibody is intrinsically linked to the epitope it engages. Clonal clustering methods, based on sequence identity, are commonly used to group antibodies that will bind to the same epitope. However, such methods neglect the fact that antibodies with highly diverse sequences can exhibit similar binding site geometries and engage common epitopes. In a previous study, we described SPACE1, a method that structurally clustered antibodies in order to predict their epitopes. This methodology was limited by the inaccuracies and incomplete coverage of template-based modeling. In addition, it was only benchmarked at the level of domain-consistency on one virus class. Here, we present SPACE2, which uses the latest machine learning-based structure prediction technology combined with a novel clustering protocol, and benchmark it on binding data that have epitope-level resolution. On six diverse sets of antigen-specific antibodies, we demonstrate that SPACE2 accurately clusters antibodies that engage common epitopes and achieves far higher dataset coverage than clonal clustering and SPACE1. Furthermore, we show that the functionally consistent structural clusters identified by SPACE2 are even more diverse in sequence, genetic lineage, and species origin than those found by SPACE1. These results reiterate that structural data improve our ability to identify antibodies that bind to the same epitope, adding information to sequence-based methods, especially in datasets of antibodies from diverse sources. SPACE2 is openly available on GitHub (https://github.com/oxpig/SPACE2).
Unraveling the role of thermal fluctuations on the exciton structure of the cryptophyte PC612 and PC645 photosynthetic antenna complexes
Authors: Ozaydin Beste , Curutchet Carles
Published: September 2023

Protein scaffolds play a crucial role in tuning the light harvesting properties of photosynthetic pigment-protein complexes, influencing pigment-protein and pigment-pigment excitonic interactions. Here, we investigate the influence of thermal dynamic effects on the protein tuning mechanisms of phycocyanin PC645 and PC612 antenna complexes of cryptophyte algae, featuring closed or open quaternary structures. We employ a dual molecular dynamics (MD) strategy that combines extensive classical MD simulations with multiple short Born-Oppenheimer quantum/molecular mechanical (QM/MM) simulations to accurately account for both static and dynamic disorder effects. Additionally, we compare the results with an alternative protocol based on multiple QM/MM geometry optimizations of the pigments. Subsequently, we employ polarizable QM/MM calculations using time-dependent density functional theory (TD-DFT) to compute the excited states, and we adopt the full cumulant expansion (FCE) formalism to describe the absorption and circular dichroism spectra. Our findings indicate that thermal effects have only minor impacts on the energy ladder in PC612, despite its remarkable flexibility owing to an open quaternary structure. In striking contrast, thermal effects significantly influence the properties of PC645 due to the absence of a hydrogen bond controlling the twist of ring D in PCB β82 bilins, as well as the larger impact of fluctuations on the excited states of MBV pigments, which possess a higher conjugation length compared to other bilin types. Overall, the dual MD protocol combined with the FCE formalism yields excellent spectral properties for PC612 and PC645, and the resultant excitonic Hamiltonians pave the way for future investigations concerning the implications of open and closed quaternary structures on phycocyanin light harvesting properties.
Evaluation of ferritin and TfR level in plasma neural-derived exosomes as potential markers of Parkinson’s disease
Authors: Chen Zhi-ting , Pan Chu-zhui , Ruan Xing-lin , Lei Li-ping , Lin Sheng-mei , Wang Yin-zhou , Zhao Zhen-Hua
Published: September 2023

Introduction

Early diagnosis of Parkinson’s disease (PD) remains challenging. It has been suggested that abnormal brain iron metabolism leads to excessive iron accumulation in PD, although the mechanism of iron deposition is not yet fully understood. Ferritin and transferrin receptor (TfR) are involved in iron metabolism, and the exosome pathway is one mechanism by which ferritin is transported and regulated. While the blood of healthy animals contains a plentiful supply of TfR positive exosomes, rare study has examined ferritin and TfR in plasma neural-derived exosomes in PD.

Methods

Plasma exosomes were obtained from 43 patients with PD and 34 healthy controls. Neural-derived exosomes were isolated with anti-human L1CAM antibody immunoabsorption. Transmission electron microscopy and western blotting were used to identify the exosomes. ELISAs were used to quantify ferritin and TfR levels in plasma neural-derived exosomes of patients with PD and controls. Receivers operating characteristic (ROC) curves were applied to map the diagnostic accuracy of ferritin and TfR. Independent predictors of the disease were identified using logistic regression models.

Results

Neural-derived exosomes exhibited the typical exosomal morphology and expressed the specific exosome marker CD63. Ferritin and TfR levels in plasma neural-derived exosomes were significantly higher in patients with PD than controls (406.46 ± 241.86 vs. 245.62 ± 165.47 ng/μg, P = 0.001 and 1728.94 ± 766.71 vs. 1153.92 ± 539.30 ng/μg, P < 0.001, respectively). There were significant positive correlations between ferritin and TfR levels in plasma neural-derived exosomes in control group, PD group and all the individuals (rs = 0.744, 0.700, and 0.752, respectively). The level of TfR was independently associated with the disease (adjusted odds ratio 1.002; 95% CI 1.000–1.003). ROC performances of ferritin, TfR, and their combination were moderate (0.730, 0.812, and 0.808, respectively). However, no relationship was found between the biomarkers and disease progression.

Conclusion

It is hypothesized that ferritin and TfR in plasma neural-derived exosomes may be potential biomarkers for PD, and that they may participate in the mechanism of excessive iron deposition in PD.
Human deprivation amblyopia: treatment insights from animal models
Authors: Duffy Kevin R. , Bear Mark F. , Patel Nimesh B. , Das Vallabh E. , Tychsen Lawrence
Published: September 2023

Amblyopia is a common visual impairment that develops during the early years of postnatal life. It emerges as a sequela to eye misalignment, an imbalanced refractive state, or obstruction to form vision. All of these conditions prevent normal vision and derail the typical development of neural connections within the visual system. Among the subtypes of amblyopia, the most debilitating and recalcitrant to treatment is deprivation amblyopia. Nevertheless, human studies focused on advancing the standard of care for amblyopia have largely avoided recruitment of patients with this rare but severe impairment subtype. In this review, we delineate characteristics of deprivation amblyopia and underscore the critical need for new and more effective therapy. Animal models offer a unique opportunity to address this unmet need by enabling the development of unconventional and potent amblyopia therapies that cannot be pioneered in humans. Insights derived from studies using animal models are discussed as potential therapeutic innovations for the remediation of deprivation amblyopia. Retinal inactivation is highlighted as an emerging therapy that exhibits efficacy against the effects of monocular deprivation at ages when conventional therapy is ineffective, and recovery occurs without apparent detriment to the treated eye.
A juvenile mouse model of anti-N-methyl-D-aspartate receptor encephalitis by active immunization
Authors: He Shuyu , Sun Chongyang , Zhu Qian , Li Lin , Huang Jianyu , Wu Ge , Cao Yi , Liao Jianxiang , Lu Yi , Su Qiru , Lin Sufang , Ma Xiaopeng , Zhong Cheng
Published: September 2023

Introduction

Anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis is a common autoimmune encephalitis, and it is associated with psychosis, dyskinesia, and seizures. Anti-NMDAR encephalitis (NMDARE) in juveniles and adults presents different clinical charactreistics. However, the pathogenesis of juvenile anti-NMDAR encephalitis remains unclear, partly because of a lack of suitable animal models.

Methods

We developed a model of juvenile anti-NMDAR encephalitis using active immunization with an amino terminal domain peptide from the GluN1 subunit (GluN1356 − 385) against NMDARs in 3-week-old female C57BL/6J mice.

Results

Immunofluorescence staining suggested that autoantibody levels in the hippocampus increased, and HEK-293T cells staining identified the target of the autoantibodies as GluN1, suggesting that GluN1-specific immunoglobulin G was successfully induced. Behavior assessment showed that the mice suffered significant cognition impairment and sociability reduction, which is similar to what is observed in patients affected by anti-NMDAR encephalitis. The mice also exhibited impaired long-term potentiation in hippocampal CA1. Pilocarpine-induced epilepsy was more severe and had a longer duration, while no spontaneous seizures were observed.

Conclusion

The juvenile mouse model for anti-NMDAR encephalitis is of great importance to investigate the pathological mechanism and therapeutic strategies for the disease, and could accelerate the study of autoimmune encephalitis.
The miRNA transcriptome of cerebrospinal fluid in preterm infants reveals the signaling pathways that promote reactive gliosis following cerebral hemorrhage
Authors: Gialeli Andriana , Spaull Robert , Plösch Torsten , Uney James , Llana Oscar Cordero , Heep Axel
Published: September 2023

Introduction

Germinal Matrix-Intraventricular Haemorrhage (GM-IVH) is one of the most common neurological complications in preterm infants, which can lead to accumulation of cerebrospinal fluid (CSF) and is a major cause of severe neurodevelopmental impairment in preterm infants. However, the pathophysiological mechanisms triggered by GM-IVH are poorly understood. Analyzing the CSF that accumulates following IVH may allow the molecular signaling and intracellular communication that contributes to pathogenesis to be elucidated. Growing evidence suggests that miRs, due to their key role in gene expression, have a significant utility as new therapeutics and biomarkers.

Methods

The levels of 2,083 microRNAs (miRs) in 15 CSF samples from 10 infants with IVH were measured using miRNA whole transcriptome sequencing. Gene ontology (GO) and miR family analysis were used to uncover dysregulated signalling which were then validated in vitro in human foetal neural progenitor cells treated with IVH-CSF.

Results

Five hundred eighty-seven miRs were differentially expressed in the CSF extracted at least 2 months after injury, compared to CSF extracted within the first month of injury. GO uncovered key pathways targeted by differentially expressed miRs including the MAPK cascade and the JAK/STAT pathway. Astrogliosis is known to occur in preterm infants, and we hypothesized that this could be due to abnormal CSF-miR signaling resulting in dysregulation of the JAK/STAT pathway – a key controller of astrocyte differentiation. We then confirmed that treatment with IVH-CSF promotes astrocyte differentiation from human fetal NPCs and that this effect could be prevented by JAK/STAT inhibition. Taken together, our results provide novel insights into the CSF/NPCs crosstalk following perinatal brain injury and reveal novel targets to improve neurodevelopmental outcomes in preterm infants.
Nomogram combining clinical and radiological characteristics for predicting the malignant probability of solitary pulmonary nodules measuring ≤ 2 cm
Authors: Xue Mengchao , Li Rongyang , Wang Kun , Liu Wen , Liu Junjie , Li Zhenyi , Ma Zheng , Zhang Huiying , Tian Hui , Tian Yu
Published: September 2023

Background

At present, how to identify the benign or malignant nature of small (≤ 2 cm) solitary pulmonary nodules (SPN) are an urgent clinical challenge. This retrospective study aimed to develop a clinical prediction model combining clinical and radiological characteristics for assessing the probability of malignancy in SPNs measuring ≤ 2 cm.

Method

In this study, we included patients with SPNs measuring ≤ 2 cm who underwent pulmonary resection with definite pathology at Qilu Hospital of Shandong University from January 2020 to December 2021. Clinical features, preoperative biomarker results, and computed tomography characteristics were collected. The enrolled patients were randomized at a ratio of 7:3 into a training cohort of 775 and a validation cohort of 331. The training cohort was used to construct the predictive model, while the validation cohort was used to test the model independently. Univariate and multivariate logistic regression analyses were performed to identify independent risk factors. The prediction model and nomogram were established based on the independent risk factors. The receiver operating characteristic (ROC) curve was used to evaluate the identification ability of the model. The calibration power was evaluated using the Hosmer–Lemeshow test and calibration curve. The clinical utility of the nomogram was also assessed by decision curve analysis (DCA).

Result

A total of 1,106 patients were included in this study. Among them, the malignancy rate of SPNs was 85.08% (941/1,106). We finally identified the following six independent risk factors by logistic regression: age, carcinoembryonic antigen, nodule shape, calcification, maximum diameter, and consolidation-to-tumor ratio. The area under the ROC curve (AUC) for the training cohort was 0.764 (95% confidence interval [CI]: 0.714–0.814), and the AUC for the validation cohort was 0.729 (95% CI: 0.647–0.811), indicating that the prediction accuracy of nomogram was relatively good. The calibration curve of the predictive model also demonstrated a good calibration in both cohorts. DCA proved that the clinical prediction model was useful in clinical practice.

Conclusion

We developed and validated a predictive model and nomogram for estimating the probability of malignancy in SPNs measuring ≤ 2 cm. With the application of predictive models, thoracic surgeons can make more rational clinical decisions while avoiding overtreatment and wasting medical resources.
C22 disrupts embryogenesis and extends C. elegans lifespan
Authors: Beydoun Safa , Sridhar Aditya , Tuckowski Angela M. , Wang Emily , Leiser Scott F.
Published: September 2023

Caenorhabditis elegans is an instrumental model in aging research due to its large brood size, short lifespan, and malleable genetics. However, maintaining a synchronous nematode population for longevity studies is challenging and time consuming due to their quick rate of development and reproduction. Multiple methods are employed in the field, ranging from worm strains with temperature dependent sterility to DNA replication inhibitors such as 5′-fluorodeoxyuridine (FUdR). In this study, we characterize a small molecule (C22) that impairs eggshell integrity and disrupts early embryogenesis to determine its applicability as a potential FUdR alternative. We find that C22 prevents egg hatching in a concentration dependent manner. However, it extends the lifespan of wild type worms and can induce FMO-2, a longevity regulating enzyme downstream of dietary restriction. Our results suggest that C22 is unlikely to be widely useful as an alternative to FUdR but its mechanism for lifespan extension may be worth further investigation.
High-throughput and separating-free phenotyping method for on-panicle rice grains based on deep learning
Authors: Lu Yuwei , Wang Jinhu , Fu Ling , Yu Lejun , Liu Qian
Published: September 2023

Rice is a vital food crop that feeds most of the global population. Cultivating high-yielding and superior-quality rice varieties has always been a critical research direction. Rice grain-related traits can be used as crucial phenotypic evidence to assess yield potential and quality. However, the analysis of rice grain traits is still mainly based on manual counting or various seed evaluation devices, which incur high costs in time and money. This study proposed a high-precision phenotyping method for rice panicles based on visible light scanning imaging and deep learning technology, which can achieve high-throughput extraction of critical traits of rice panicles without separating and threshing rice panicles. The imaging of rice panicles was realized through visible light scanning. The grains were detected and segmented using the Faster R-CNN-based model, and an improved Pix2Pix model cascaded with it was used to compensate for the information loss caused by the natural occlusion between the rice grains. An image processing pipeline was designed to calculate fifteen phenotypic traits of the on-panicle rice grains. Eight varieties of rice were used to verify the reliability of this method. The R2 values between the extraction by the method and manual measurements of the grain number, grain length, grain width, grain length/width ratio and grain perimeter were 0.99, 0.96, 0.83, 0.90 and 0.84, respectively. Their mean absolute percentage error (MAPE) values were 1.65%, 7.15%, 5.76%, 9.13% and 6.51%. The average imaging time of each rice panicle was about 60 seconds, and the total time of data processing and phenotyping traits extraction was less than 10 seconds. By randomly selecting one thousand grains from each of the eight varieties and analyzing traits, it was found that there were certain differences between varieties in the number distribution of thousand-grain length, thousand-grain width, and thousand-grain length/width ratio. The results show that this method is suitable for high-throughput, non-destructive, and high-precision extraction of on-panicle grains traits without separating. Low cost and robust performance make it easy to popularize. The research results will provide new ideas and methods for extracting panicle traits of rice and other crops.
The impact of vegetation phenology changes on the relationship between climate and net primary productivity in Yunnan, China, under global warming
Authors: Chen Xu , Zhang Yaping
Published: September 2023

Climate influences net primary productivity (NPP) either directly or indirectly via phenology. Therefore, clarifying the indirect effects of climate on NPP through phenology is of utmost importance. However, the underlying mechanisms by which phenology indirectly affects NPP are unknown and poorly studied. Based on different structural equation models, this study analyzed the influence of phenology on the relationship between climate and NPP, and the results were as follows: (1) Temperature and solar radiation directly affect the end and beginning of the growing season, respectively, while precipitation indirectly affects the beginning of the growing season. (2) Spring phenology mainly affects the relationship between subsequent precipitation and net primary productivity, while autumn phenology mainly affects the relationship between temperature and net primary productivity. (3) Solar radiation is the most important direct influence factor on phenology and NPP, and the relationship between it and NPP is hardly disturbed by vegetation phenology. This research holds significant scientific and applied values in enhancing our understanding of the effects of global warming, forecasting ecosystem responses in the future, and formulating adaptation strategies.
Genetic and molecular understanding for the development of methionine-rich maize: a holistic approach
Authors: Devi Veena , Bhushan Bharat , Gupta Mamta , Sethi Mehak , Kaur Charanjeet , Singh Alla , Singh Vishal , Kumar Ramesh , Rakshit Sujay , Chaudhary Dharam P.
Published: September 2023

Maize (Zea mays) is the most important coarse cereal utilized as a major energy source for animal feed and humans. However, maize grains are deficient in methionine, an essential amino acid required for proper growth and development. Synthetic methionine has been used in animal feed, which is costlier and leads to adverse health effects on end-users. Bio-fortification of maize for methionine is, therefore, the most sustainable and environmental friendly approach. The zein proteins are responsible for methionine deposition in the form of δ-zein, which are major seed storage proteins of maize kernel. The present review summarizes various aspects of methionine including its importance and requirement for different subjects, its role in animal growth and performance, regulation of methionine content in maize and its utilization in human food. This review gives insight into improvement strategies including the selection of natural high-methionine mutants, molecular modulation of maize seed storage proteins and target key enzymes for sulphur metabolism and its flux towards the methionine synthesis, expression of synthetic genes, modifying gene codon and promoters employing genetic engineering approaches to enhance its expression. The compiled information on methionine and essential amino acids linked Quantitative Trait Loci in maize and orthologs cereals will give insight into the hotspot-linked genomic regions across the diverse range of maize germplasm through meta-QTL studies. The detailed information about candidate genes will provide the opportunity to target specific regions for gene editing to enhance methionine content in maize. Overall, this review will be helpful for researchers to design appropriate strategies to develop high-methionine maize.
Application fruit tree hole storage brick fertilizer is beneficial to increase the nitrogen utilization of grape under subsurface drip irrigation
Authors: Yao Dongdong , Yang Jianli , Jia Haifeng , Zhou Yufan , Lv Qi , Li Xujiao , Zhang Huanhuan , Fesobi Phillip , Liu Huaifeng , Zhao Fengyun , Yu Kun
Published: September 2023

It is very important to promote plant growth and decrease the nitrogen leaching in soil, to improve nitrogen (N) utilization efficiency. In this experiment, we designed a new fertilization strategy, fruit tree hole storage brick (FTHSB) application under subsurface drip irrigation, to characterise the effects of FTHSB addition on N absorption and utilization in grapes. Three treatments were set in this study, including subsurface drip irrigation (CK) control, fruit tree hole storage brick A (T1) treatment, and fruit tree hole storage brick B (T2) treatment. Results showed that the pore number and size of FTHSB A were significantly higher than FTHSB B. Compared with CK, T1 and T2 treatments significantly increased the biomass of different organs of grape, N utilization and 15N content in the roots, stems and leaves, along with more prominent promotion at T1 treatment. When the soil depth was 15–30 cm, the FTHSB application significantly increased the soil 15N content. But when the soil depth was 30–45 cm, it reduced the soil 15N content greatly. T1 and T2 treatments obviously increased the activities of nitrite reductase (NR) and glutamine synthetase (GS) in grape leaves, also the urease activity(UR) in 30 cm of soil. Our findings suggest that FTHSB promoted plant N utilization by reducing N loss in soil and increasing the enzyme activity related to nitrogen metabolism. In addition, this study showed that FTHSB A application was more effective than FTHSB B in improving nitrogen utilization in grapes.
Measuring what matters in healthcare: a practical guide to psychometric principles and instrument development
Authors: Swan Katina , Speyer Renee , Scharitzer Martina , Farneti Daniele , Brown Ted , Woisard Virginie , Cordier Reinie
Published: September 2023

The provision of quality healthcare relies on scales and measures with robust evidence of their psychometric properties. Using measurement instruments with poor reliability, validity, or feasibility, or those that are not appropriate for the target diagnostic group or construct/dimension under consideration, may be unfavorable for patients, unproductive, and hinder empirical advancement. Resources from the COnsensus-based Standards for the selection of health status Measurement INstruments (COSMIN) group can assist in identifying and developing psychometrically sound measures. The COSMIN initiative is the only international, research-based practice taxonomy and methodological guidelines for measurement in healthcare. This manuscript aims to provide an accessible introduction to theories, principles and practices of psychometrics, instrument properties, and scale development, with applied examples from the COSMIN recommendations. It describes why measurement in healthcare is critical to good practice, explains the concepts of the latent variable and hypothetical construct and their importance in healthcare assessments, explores issues of flawed measurement and briefly explains key theories relevant to psychometrics. The paper also outlines a ten-step process to develop and validate a new measurement instrument, with examples drawn from a recently developed visuoperceptual measure for analysis of disordered swallowing to demonstrate key concepts and provides a guide for understanding properties of and terminology related to measurement instruments. This manuscript serves as a resource for healthcare clinicians, educators, and researchers who seek to develop and validate new measurement instruments or improve the properties of existing ones. It highlights the importance of using psychometrically sound measurement instruments to ensure high-quality healthcare assessments.
The shift from quantitative to qualitative thinking—problems and prospects as viewed from Husserl’s and Hegel’s philosophy
Authors: Gutland Christopher
Published: September 2023

This article contrasts the views of the philosophers Husserl and Hegel on quantification in science and compares their proposals for conducting rigorous qualitative research. Both deem quantification integral to science, but furthermore proposed methodologies to investigate qualitative necessities achieved by a shift in conscious activity and awareness. However, their methodologies differ significantly. While Husserl rejects idealization and instead proposes intuitive means to ideate qualitative essential relations, Hegel suggests idealizing less one-sidedly, namely, qualitatively over and above quantitatively. The article first examines how quantification is achieved and how it contrasts with measuring. This contrast reveals that measuring implies knowledge of qualities. These qualities, however, thus far remain oddly external to the mathematical relations linking the various established equations. The article then follows Husserl’s reconstruction of the development of science to illustrate the dismissal of many experiential qualities and how philosophy further amplified skepticism about science on qualities. Husserl’s notion of the life-world and the method of eidetic variation are then introduced as means to counterbalance mathematical proceedings in science. However, this method reveals both eidetic qualitative structures and psychical structures without being able to distinguish between them. It is thus susceptible to idiosyncratic, traditional, and cultural biases. Subsequently, Hegel’s description of the shift in conscious experience that sets qualitative from quantitative thinking apart is introduced. This shift may overcome the biases, but it faces skepticism that calls for further investigation of the experience of different kinds of thinking.
Taiwanese parents’ perspectives on young children’s use of information communication technology
Authors: Luo Yi Fang , Yang Shu Ching , Chou Kun Yi , Lee Hsin Tien
Published: September 2023

Introduction

How parents think and feel about their children’s use of technology can influence how their kids behave online. The family’s socioeconomic status (SES) may also affect this influence. In light of this, this research emphasizes the need for more investigation into parental attitudes and the role of SES in shaping how children consume media.

Methods

This study surveyed 629 Taiwanese parents to explore their attitudes toward their young children’s use of information communication technology (ICT), usage patterns, and the interplay with socioeconomic status.

Results

The findings revealed a significant disconnect: although approximately 50% of parents considered above six years old to be a suitable age for children to start ICT, over 80% of children had already engaged with ICT before that age, indicating a large disparity between parental expectations and actual initiation. Furthermore, parents highlighted “learning interest” and “various content” as the most positive impacts of children’s ICT use, while “addiction and overreliance” emerged as their primary concern. Notably, parents, as a whole, tended to perceive their child’s ICT use more negative than positively, with fathers displaying greater acceptance of negative viewpoints than mothers. Parental attitudes toward children’s ICT use were categorized into five clusters, ranging from balanced and optimistic views to value emphasis, conservatism, and negative doubts. This classification underscores the intricate and multifaceted nature of parental perspectives, encompassing both positive and negative outlooks on children’s ICT utilization.

Discussion

The findings underscore the nuanced character of parents’ attitudes toward technology, shaped by the intricacies and challenges posed by the digital era. These insights emphasize that parental attitudes go beyond a simplistic positive-negative divide, reflecting a comprehensive response to the opportunities and complexities inherent in the digital age.
Inner Peace needs of male psychiatric patients in post-war Croatia are associated with their needs to clarify open issues in their life and their needs for forgiveness
Authors: Glavas Andrijana , Büssing Arndt , Baumann Klaus
Published: September 2023

Background

More than 25 years after the end of the Balkan war, many people belonging to the post-war population are still traumatized by the war events and have been treated for post-traumatic stress disorder or other psychiatric diagnoses. We were interested in their Inner Peace needs, how these relate to indicators of mental health, and their needs to clarify open processes in their lives and to forgive and be forgiven.

Materials and methods

In a cross-sectional survey with standardized questionnaires (i.e., SpNQ, PCL-M, HADS, and BMLSS), 638 male patients who were treated in seven psychiatric centers in Croatia were enrolled. 68% were diagnosed with PTSD and 32% had other psychiatric diagnoses. Most had actively participated in the Balkan war (79%), and 60% for the whole war period.

Results

Strong needs to “immerse into beauty of nature” were stated by 47%, to “dwell at a place of quietness and peace” by 66%, and to “find inner peace” by 57%. These Inner Peace needs were highest in men treated with PTSD diagnoses as compared to men with other psychiatric diagnoses and were slightly lower in men who were active during the whole war period as compared to shorter phases of war participation. Regression analyses with Inner Peace needs as a dependent variable revealed that Clarification/Forgiveness needs were the best predictor, with further influences of PTSD symptoms and life satisfaction, explaining altogether 49% of the variance. The best predictors of their PTSD symptoms were life satisfaction, perceived burden, depressive symptoms, Inner Peace needs, religious trust, and duration of war participation, explaining 60% of the variance.

Conclusion

In Croatian male war participants in clinical treatment decades after the war, Inner Peace needs indicate their ongoing intention to let go of their disturbing experiences and to find states of inner peace, particularly at specific places of quietness and peace. These needs can be considered metaphors for longing for wholeness, integrity, and safety, in contrast to the ongoing impact of unresolved issues. Thus, apart from psychotherapeutic treatment, sheltered places of nature, inspiration, and reconciliation might be elements to improve the difficult situation of post-war victims still suffering from their experiences.