bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-modular structure of the gene regulatory network for specification and commitment of murine T cells
Authors: Shin Boyoung , Rothenberg Ellen V.
Published: January 2023

T cells develop from multipotent progenitors by a gradual process dependent on intrathymic Notch signaling and coupled with extensive proliferation. The stages leading them to T-cell lineage commitment are well characterized by single-cell and bulk RNA analyses of sorted populations and by direct measurements of precursor-product relationships. This process depends not only on Notch signaling but also on multiple transcription factors, some associated with stemness and multipotency, some with alternative lineages, and others associated with T-cell fate. These factors interact in opposing or semi-independent T cell gene regulatory network (GRN) subcircuits that are increasingly well defined. A newly comprehensive picture of this network has emerged. Importantly, because key factors in the GRN can bind to markedly different genomic sites at one stage than they do at other stages, the genes they significantly regulate are also stage-specific. Global transcriptome analyses of perturbations have revealed an underlying modular structure to the T-cell commitment GRN, separating decisions to lose “stem-ness” from decisions to block alternative fates. Finally, the updated network sheds light on the intimate relationship between the T-cell program, which depends on the thymus, and the innate lymphoid cell (ILC) program, which does not.
Adverse events associated with anti-IL-17 agents for psoriasis and psoriatic arthritis: a systematic scoping review
Authors: Wang Jiao , Wang Chunxiao , Liu Liu , Hong Seokgyeong , Ru Yi , Sun Xiaoying , Chen Jiale , Zhang Miao , Lin Naixuan , Li Bin , Li Xin
Published: January 2023

Background

Anti-interleukin (IL)-17 biological agents (BAs) have significant efficacy in the treatment of psoriasis and psoriatic arthritis; however, adverse events (AEs) are common, and their safety has not been systematically evaluated.

Objectives

The purpose of this systematic review and meta-analysis was to summarize the number and corresponding rates of AEs caused by anti-IL-17 BAs in patients with psoriasis and psoriatic arthritis to improve clinical decision-making regarding their use.

Methods

PubMed, Embase, Cochrane Library, and Web of Science databases were independently searched by three authors for articles on the treatment of psoriasis with anti-IL-17 BAs that were published before March 1, 2022, and included at least one AE. Dichotomous variables and 95% confidence intervals (CI) were analyzed using R software (version 4.1.3) and the Meta and Metafor software packages. Funnel plots and meta-regression were used to test for the risk of bias, I2 was used to assess the magnitude of heterogeneity, and subgroup analysis was used to reduce heterogeneity.

Results

A total of 57 studies involving 28,424 patients with psoriasis treated with anti-IL-17 BAs were included in the meta-analysis. Subgroup analysis showed that anti-IL-17A (73.48%) and anti-IL-17A/F (73.12%) BAs were more likely to cause AEs than anti-IL-17R BAs (65.66%). The incidence of AEs was as high as 72.70% with treatment durations longer than one year, and long-term use of medication had the potential to lead to mental disorders. Infection (33.16%), nasopharyngitis (13.74%), and injection site reactions (8.28%) were the most common AEs. Anti-IL-17 BAs were most likely to cause type α (33.52%) AEs. Type δ AEs (1.01%) were rarely observed.

Conclusions

Anti-IL-17 BAs used for the treatment of psoriasis and psoriatic arthritis caused a series of AEs, but the symptoms were generally mild.
Metabolomics for biomarker discovery in schistosomiasis: A systematic scoping review
Authors: Midzi Herald , Vengesai Arthur , Muleya Victor , Kasambala Maritha , Mduluza-Jokonya Tariro Lavender , Chipako Isaac , Siamayuwa Clayton Edmore , Mutapi Francisca , Naicker Thajasvarie , Mduluza Takafira
Published: January 2023

Background

Metabolomic based approaches are essential tools in the discovery of unique biomarkers for infectious diseases via high-throughput global assessment of metabolites and metabolite pathway dysregulation. This in-turn allows the development of diagnostic tools and provision of therapeutics. In this review, we aimed to give an overview of metabolite biomarkers and metabolic pathway alterations during Schistosoma haematobium and Schistosoma mansoni infections.

Methods

We conducted the review by systematically searching electronic databases and grey literature to identify relevant metabolomics studies on schistosomiasis. Arksey and O’Malley methodology for conducting systematic scoping reviews was applied. A narrative summary of results was conducted following the Preferred Reporting Items for Systematic reviews and Meta-Analyses extension for scoping review guidelines.

Results

Twelve articles included in the review identified 127 metabolites, whose concentrations were considerably altered during S. mansoni and S. haematobium infections. The metabolites were assigned to metabolic pathways involved in energy (34.6%), gut microbial (11.0%), amino acid (25.2%), nucleic acids (6.3%), immune proteins (8.7%) hormones (2.4%) and structural proteins/lipids (11.8%). Energy related metabolic pathways were the most affected during schistosome infections with metabolites such as succinate, citrate, aconitate and fumarate of the tricarbocylic acid cycle being significantly altered in organ, serum and plasma samples. Amino acid metabolism was also impacted during schistosome infections as phenylacetylglycine, alanine, taurine, 2-oxoisocaproate and 2-oxoisovalerate emerged as potent biomarkers. Elevated structural proteins such as actin, collagen and keratin concentrations were identified as biomarkers of liver fibrosis, a common pathological feature in chronic schistosomiasis infections. Hippurate was a major metabolite biomarker in the gut microbial related pathway.

Conclusions

The analysis of the literature revealed that energy related metabolic pathways are considerably altered during S. mansoni and S. haematobium infections. Therefore, their metabolites may provide biomarkers for diagnosis and prognosis in addition to providing therapeutics for parasitic infections. This scoping review has identified a need to replicate more schistosomiasis metabolomic studies in humans to complement animal-model based studies.
On the control of spatial and temporal oceanic scales by existing and future observing systems: An observing system simulation experiment approach
Authors: Gasparin Florent , Lellouche Jean-Michael , Cravatte Sophie E. , Ruggiero Giovanni , Rohith B. , Le Traon Pierre Yves , Rémy Elisabeth
Published: January 2023

Ocean monitoring and forecasting systems combine information from ocean observations and numerical models through advanced data assimilation techniques. They are essential to monitor and report on past, present and future oceanic conditions. However, given the continuous development of oceanic models and data assimilation techniques in addition to the increased diversity of assimilated platforms, it becomes more and more difficult to establish how information from observations is used, and to determine the utility and relevance of a change of the global ocean observing system on ocean analyses. Here, a series of observing system simulation experiments (OSSE), which consist in simulating synthetic observations from a realistic simulation to be subsequently assimilated in an experimental analysis system, was performed. An original multiscale approach is then used to investigate (i) the impact of various observing system components by distinguishing between satellites and in situ (Argo floats and tropical moorings), and (ii) the impact of recommended changes in observing systems, in particular the impact of Argo floats doubling and enhancements of tropical moorings, on the fidelity of ocean analyses. This multiscale approach is key to better understand how observing system components, with their distinct sampling characteristics, help to constrain physical processes. The study demonstrates the ability of the analysis system to represent 40-80% of the temperature variance at mesoscale (20-30% for salinity), and more than 80% for larger scales. Satellite information, mostly through altimetric data, strongly constrains mesoscale variability, while the impact of in situ temperature and salinity profiles are essential to constrain large scale variability. It is also shown that future enhancements of Argo and tropical mooring arrays observations will likely be beneficial to ocean analyses at both intermediate and large scales, with a higher impact for salinity-related quantities. This work provides a better understanding on the respective role of major satellite and in situ observing system components in the integrated ocean observing system.
A novel prognostic model related to oxidative stress for treatment prediction in lung adenocarcinoma
Authors: Peng Haijun , Li Xiaoqing , Luan Yanchao , Wang Changjing , Wang Wei
Published: January 2023

Background

The prognostic model based on oxidative stress for lung adenocarcinoma (LUAD) remains unclear.

Methods

The information of LUAD patients were acquired from TCGA dataset. We also collected two external datasets from GEO for verification. Oxidative stress-related genes (ORGs) were extracted from Genecards. We performed machine learning algorithms, including Univariate Cox regression, Random Survival Forest, and Least Absolute Shrinkage and Selection Operator (Lasso) analyses on the ORGs to build the OS-score and OS-signature. We drew the Kaplan-Meier and time-dependent receiver operating characteristic curve (ROC) to evaluate the efficacy of the OS-signature in predicting the prognosis of LUAD. We used GISTIC 2.0 and maftool algorithms to explore Genomic mutation of OS-signature. To analyze characteristic of tumor infiltrating immune cells, ESTIMATE, TIMER2.0, MCPcounter and ssGSEA algorithms were applied, thus evaluating the immunotherapeutic strategies. Chemotherapeutics sensitivity analysis was based on pRRophetic package. Finally, PCR assays was also used to detect the expression values of related genes in the OS-signature in cell lines.

Results

Ten ORGs with prognostic value and the OS-signature containing three prognostic ORGs were identified. The significantly better prognosis of LUAD patients was observed in LUAD patients. The efficiency and accuracy of OS-signature in predicting prognosis for LUAD patients was confirmed by survival ROC curves and two external validation data sets. It was clearly observed that patients with high OS-scores had lower immunomodulators levels (with a few exceptions), stromal score, immune score, ESTIMATE score and infiltrating immune cell populations. On the contrary, patients with higher OS-scores were more likely to have higher tumor purity. PCR assays showed that, MRPL44 and CYCS were significantly higher expressed in LUAD cell lines, while CAT was significantly lower expressed.

Conclusion

The novel oxidative stress-related model we identified could be used for prognosis and treatment prediction in lung adenocarcinoma.
The optimal regional irradiation volume for breast cancer patients: A comprehensive systematic review and network meta-analysis of published studies
Authors: Qi Wei-Xiang , Cao Lu , Xu Cheng , Cai Gang , Chen Jiayi
Published: January 2023

Background

Currently, the optimal adjuvant regional nodal irradiation (RNI) volume for breast cancer (BC) remained controversial. We aimed to define the optimal RNI treatment volume for BC by using a comprehensive network meta-analysis (NMA) of published studies.

Materials and methods

PubMed, Embase, Medline, and Cochrane Central Register of Controlled Trials were searched from database inception to 30 May 2022. Studies assessing different adjuvant RNI volumes for BC were eligible for inclusion. The primary outcome was overall survival (OS), and secondary outcome was disease-free survival (DFS) and distant-metastasis-free survival (DMFS).

Results

A total of 29,640 BC patients from twenty studies were included. The pooled hazard ratio demonstrated that internal mammary node irradiation (IMNI) in BC patients significantly improved OS giving HR (hazard ratio) of 0.87 (95%CI: 0.83–0.91, p<0.001), DFS with HR of 0.78 (95%CI: 0.68–0.90, p<0.01), and DMFS with HR of 0.87 (95%CI: 0.79–0.97, p<0.01) when compared to controls. Sub-group analysis indicated that RNI with IMNI significantly improved OS (HR 0.87, 95%CI: 0.81–0.93, p<0.01), DFS (HR 0.65, 95%CI: 0.56–0.77, p<0.01), and DMFS (HR 0.90, 95%CI: 0.82–0.98, p=0.02) when compared to RNI without IMNI. NMA showed that CW/WB (chest wall/whole breast) + RNI with IMNI significantly improved DFS (HR 0.93, 95%CI: 0.86–1.00) and DMFS (HR 0.90, 95%CI: 0.81–0.99), but not for OS (HR 0.93, 95%CI: 0.84–1.03) when compared to CW/WB alone. Based on the analysis of the treatment ranking, CW/WB+RNI with IMNI appeared as the best treatment approach for BC patients.

Conclusions

Our pooled results demonstrated that RNI with IMNI yielded a significant survival advantage for BC patients. NMA showed that CW/WB+RNI with IMNI was the optimal radiation volume for BC patients.
Monoparametric high-resolution diffusion weighted MRI as a possible first step in an MRI-directed diagnostic pathway for men with suspicion of prostate cancer
Authors: Reijnen Jeroen Sebastiaan , Ryg Una , Marthinsen Jon B. , Schönhardt Irina , Seierstad Therese , Hole Knut H.
Published: January 2023

Purpose

To explore if a high-resolution diffusion weighted MRI sequence (DWI-only) could be used as a first step in an MRI-directed diagnostic pathway.

Methods

Prospective single center study that between December 2017 and August 2018 included 129 consecutive patients with suspicion of prostate cancer into a PI-RADS-based MRI-directed diagnostic pathway. All patients had multiparametric MRI (mpMRI). Based on only the transversal high-resolution DWI images two consultant radiologists prospectively categorized the findings as positive, equivocal, or negative for clinically significant cancer. The radiologists then interpreted the mpMRI and assigned a PI-RADS score. A third independent reader retrospectively categorized the DWI-only exams without access to the mpMRI. The interpretations of DWI-only were compared to the PI-RADS classification from mpMRI and the histopathology from the biopsies. Non-biopsied patients were followed in a safety net monitoring for 56 months.

Results

Based on DWI-only, 29 (22.5%) of the exams were categorized as negative, 38 (29.5%) as equivocal and 62 (48.1%) as positive. Of the 56 patients with PI-RADS 4-5 at mpMRI, 55 were also categorized as positive at DWI-only. All patients diagnosed with clinically significant cancer were identified using DWI-only. 56 months of safety net monitoring did not reveal any clinically significant cancers among patients with exams categorized as negative or equivocal. There was high inter-reader agreement on positive findings, but less agreement on negative and equivocal findings.

Conclusions

In this concept study, the monoparametric DWI-only identified all patients with clinically significant cancer in a mpMRI-directed diagnostic pathway.
Preoperative prognostic prediction for stage I lung adenocarcinomas: Impact of the computed tomography features associated with the new histological grading system
Authors: Liang Min , Tang Wei , Tan Fengwei , Zeng Hui , Guo Changyuan , Feng Feiyue , Wu Ning
Published: January 2023

Objectives

This study aimed to identify the computed tomography (CT) features associated with the new International Association for the Study of Lung Cancer (IASLC) three-tiered grading system to improve the preoperative prediction of disease-free survival of stage I lung adenocarcinoma patients.

Methods

The study included 379 patients. Ordinal logistic regression analysis was used to identify the independent predictors of IASLC grades. The first multivariate Cox regression model (Model 1) was based on the significant factors from the univariate analysis. The second multivariate model (Model 2) excluded the histologic grade and based only on preoperative factors.

Results

Larger consolidation tumor ratio (OR=2.15, P<.001), whole tumor size (OR=1.74, P=.002), and higher CT value (OR=3.77, P=.001) were independent predictors of higher IASLC grade. Sixty patients experienced recurrences after 70.4 months of follow-up. Model 1 consisted of age (HR:1.05, P=.003), clinical T stage (HR:2.32, P<.001), histologic grade (HR:4.31, P<.001), and burrs sign (HR:5.96, P<.001). Model 2 consisted of age (HR,1.04; P=.015), clinical T stage (HR:2.49, P<.001), consolidation tumor ratio (HR:2.49, P=.016), whole tumor size (HR:2.81, P=.022), and the burrs sign (HR:4.55, P=.002). Model 1 had the best prognostic predictive performance, followed by Model 2, clinical T stage, and histologic grade.

Conclusion

CTR (cut-off values of <25% and ≥75%) and whole tumor size (cut-off value of 17 mm) could stratify patients into different prognosis and be used as preoperative surrogates for the IASLC grading system. Integrating these CT features with clinical T staging can improve the preoperative prognostic prediction for stage I lung adenocarcinoma patients.
A CT-based radiomics approach to predict immediate response of radiofrequency ablation in colorectal cancer lung metastases
Authors: Huang Haozhe , Zheng Dezhong , Chen Hong , Chen Chao , Wang Ying , Xu Lichao , Wang Yaohui , He Xinhong , Yang Yuanyuan , Li Wentao
Published: January 2023

Objectives

To objectively and accurately assess the immediate efficacy of radiofrequency ablation (RFA) on colorectal cancer (CRC) lung metastases, the novel multimodal data fusion model based on radiomics features and clinical variables was developed.

Methods

This case-control single-center retrospective study included 479 lung metastases treated with RFA in 198 CRC patients. Clinical and radiological data before and intraoperative computed tomography (CT) scans were retrieved. The relative radiomics features were extracted from pre- and immediate post-RFA CT scans by maximum relevance and minimum redundancy algorithm (MRMRA). The Gaussian mixture model (GMM) was used to divide the data of the training dataset and testing dataset. In the process of modeling in the training set, radiomics model, clinical model and fusion model were built based on a random forest classifier. Finally, verification was carried out on an independent test dataset. The receiver operating characteristic curves (ROC) were drawn based on the obtained predicted scores, and the corresponding area under ROC curve (AUC), accuracy, sensitivity, and specificity were calculated and compared.

Results

Among the 479 pulmonary metastases, 379 had complete response (CR) ablation and 100 had incomplete response ablation. Three hundred eighty-six lesions were selected to construct a training dataset and 93 lesions to construct a testing dataset. The multivariate logistic regression analysis revealed cancer antigen 19-9 (CA19-9, p<0.001) and the location of the metastases (p< 0.05) as independent risk factors. Significant correlations were observed between complete ablation and 9 radiomics features. The best prediction performance was achieved with the proposed multimodal data fusion model integrating radiomic features and clinical variables with the highest accuracy (82.6%), AUC value (0.921), sensitivity (80.3%), and specificity (81.4%).

Conclusion

This novel multimodal data fusion model was demonstrated efficient for immediate efficacy evaluation after RFA for CRC lung metastases, which could benefit necessary complementary treatment.
Rice DST transcription factor negatively regulates heat tolerance through ROS-mediated stomatal movement and heat-responsive gene expression
Authors: Ding Yanfei , Zhou Mei , Wang Ke , Qu Aili , Hu Shanshan , Jiang Qiong , Yi Keke , Wang Feijuan , Cai Chong , Zhu Cheng , Chen Zhixiang
Published: January 2023

Plants are frequently subjected to a broad spectrum of abiotic stresses including drought, salinity and extreme temperatures and have evolved both common and stress-specific responses to promote fitness and survival. Understanding the components and mechanisms that underlie both common and stress-specific responses can enable development of crop plants tolerant to different stresses. Here, we report a rice heat stress-tolerant 1 (hst1) mutant with increased heat tolerance. HST1 encodes the DST transcription factor, which also regulates drought and salinity tolerance. Increased heat tolerance of hst1 was associated with suppressed expression of reactive oxygen species (ROS)-scavenging peroxidases and increased ROS levels, which reduced water loss by decreasing stomatal aperture under heat stress. In addition, increased ROS levels enhanced expression of genes encoding heat shock protein (HSPs) including HSP80, HSP74, HSP58 and small HSPs. HSPs promote stabilization of proteins and protein refolding under heat stress and accordingly mutation of HST1 also improved reproductive traits including pollen viability and seed setting under high temperature. These results broaden the negative roles of DST in abiotic stress tolerance and provide important new insights into DST-regulated tolerance to diverse abiotic stresses through both shared and stress-specific mechanisms.
Grass-legume mixture and nitrogen application improve yield, quality, and water and nitrogen utilization efficiency of grazed pastures in the loess plateau
Authors: Xu Ranran , Shi Wei , Kamran Muhammad , Chang Shenghua , Jia Qianmin , Hou Fujiang
Published: January 2023

Grazing on cultivated grassland is a green agricultural model. However, in China's Loess Plateau, the type of cultivated grassland suitable for grazing and the amount of nitrogen application is still unclear, which has led to the failure of this model to be widely implemented. In this context, we set up an experiment using three grass planting types, including monoculture of alfalfa (Medicago sativa L.), monoculture of brome (Bromus inermis L.), and mixed planting of the two forages. Under each planting type, there were six management measures: grazing and no nitrogen application (GN1), grazing and 80 kg ha-1nitrogen application (GN2), grazing and 160 kg ha-1nitrogen application (GN3), cutting and no nitrogen application (MN1), cutting and 80 kg ha-1nitrogen application (MN2), and cutting and 160 kg ha-1nitrogen application (MN3). To explore the impacts of these treatments on pastures, we studied the effects on the yield, quality, and water use efficiency of the three cultivated grasslands. Results showed that alfalfa monoculture and alfalfa-brome mixed sowing grassland resulted in significantly higher hay yield, crude protein yield, water use efficiency (WUE), precipitation use efficiency (PUE), nitrogen use efficiency (NUE), and agronomic efficiency of nitrogen (AEN) as compared to brome monoculture grassland. In addition, the crude protein, ether extract, and crude ash content of alfalfa monoculture and alfalfa-brome mixture were increased significantly while the contents of neutral detergent fiber (NDF) were reduced, thereby increasing the relative feed value (RFV) during the two years. The forage hay yield, crude protein yield, ether extract, crude ash content, RFV, PUE, and WUE were significantly higher with GN1, GN2, and GN3 treatments than that with MN1 treatment. In contrast, the NDF and acid detergent fiber (ADF) content was significantly lower than the MN1 treatment. Furthermore, the fresh forage yield, crude protein yield, PUE, and WUE of GN3 treatment were significantly higher than that of GN1 and GN2 treatments in both years, while the NUE and AEN were significantly higher in GN2 and GN3 treatments than that of MN3 treatment. Based on these results, alfalfa-brome mixed cropping with the application of 160 kg ha-1nitrogen under grazing conditions is an appropriate management practice for improving the forage yield, quality, and water- and nitrogen utilization efficiency of cultivated grassland in the Loess Plateau of China. This integrated management model is applicable to the cultivation and utilization of mixed grassland on nutrient-poor land in the Loess Plateau.
Neutrinos: The Ghost Particles That Make Up Our Universe
Authors: McDonald Art
Published: January 2023

In the field of particle astrophysics, scientists are trying to understand how the universe started and how it works at a very basic level. Using particles from astrophysics sources, we study the laws of physics at the smallest possible scale of matter and develop mathematical formulas that describe how elementary particles interact with each other to make up our universe. My colleagues and I have been studying neutrinos—one of the fundamental building blocks of the universe. That helps us understand how the universe has evolved since it began with the Big Bang some 13.8 billion years ago. In this article, I will tell you about the “ghost particles” called neutrinos—what they are, how we measure them, and why our discovery required a major change in our measurement methods. In this process, you will get to see how the most elusive elements around us are sometimes among the most important.
Resolution Revolution—Seeing the Molecules of Life With Electron Cryomicroscopy
Authors: Segev Noa , Henderson Richard
Published: January 2023

This article is based on an interview between the two authors.

Structural biology is a field that seeks to find the structures of all the components that make up living things—from molecules that exist in humans and other animals, through molecules present in tiny microorganisms, to the molecules that make up plants. To determine these structures, structural biologists use sophisticated imaging techniques that are becoming more and more accurate at “seeing”, or determining the structure of smaller and more diverse molecules. Electron cryomicroscopy is one very advanced and powerful imaging technique. In this technique, electrons are sent through frozen specimens to determine the structures of single molecules, at magnifications that are enough to see atoms. These images are taking us one step further toward understanding the structure and function of the basic building blocks of life. In this article, we will tell you about the developments that led to what is called “the resolution revolution” in electron cryomicroscopy, which Dr. Henderson was part of and that eventually allowed him to share the Nobel Prize in Chemistry in 2017.
Soil assessment in Denmark: Towards soil functional mapping and beyond
Authors: Gomes Lucas Carvalho , Beucher Amélie Marie , Møller Anders Bjørn , Iversen Bo V. , Børgesen Christen Duus , Adetsu Diana Vigah , Sechu Gasper Laurent , Heckrath Goswin Johann , Koch Julian , Adhikari Kabindra , Knadel Maria , Lamandé Mathieu , Greve Mette Balslev , Jensen Niels H. , Gutierrez Sebastian , Balstrøm Thomas , Koganti Triven , Roell Yannik , Peng Yi , Greve Mogens Humlekrog
Published: January 2023

Soil provides essential ecosystem services sustaining and improving human life, but mapping soil functions is an ongoing challenge. Denmark has a long history of carrying out soil assessments − originally in order to determine tax revenues for the king, and, more recently, for aiding policymakers and farmers. This knowledge has supported the development of intensive agricultural systems while maintaining the provision of ecosystem services (e.g., clean water). Getting an overview of historical soil surveys and pedological mapping approaches can generate useful information for mapping soil, identifying gaps and proposing directions for future research. In this review, we explore the evolution of soil and environmental inventories, the historical development of soil mapping methods, and how these factors contributed to a better spatial understanding of soil functions. Specifically, we discuss soil functions related to water regulation (e.g., drainage, groundwater and water surface interactions, water table), water filtering (e.g., nitrogen leaching), carbon sequestration (e.g., peatlands), agricultural production (e.g., land suitability, wheat yields), and threats related to soil degradation (e.g., soil erosion). Denmark has benefitted from a government-coordinated approach, promoting detailed and systematic national soil surveys and environmental monitoring programmes. The large databases produced in the surveys formed the basis for mapping several soil properties and functions at increasingly high resolutions over the last many years based on developments in machine learning. In contrast to methodological advances in soil mapping and relevant contributions to pedometric research, we identified a lack of spatial information on soil biodiversity. Detailed spatial information about soil functions is essential to address global issues, such as climate change, food security and water security, and the experience of mapping soil functions in Denmark can be a source of inspiration to other parts of the world.
FACILITATE: A real-world, multicenter, prospective study investigating the utility of a rapid, fully automated real-time PCR assay versus local reference methods for detecting epidermal growth factor receptor variants in NSCLC
Authors: Behnke Anke , Cayre Anne , De Maglio Giovanna , Giannini Giuseppe , Habran Lionel , Tarsitano Marina , Chetta Massimiliano , Cappellen David , Lespagnol Alexandra , Le Naoures Cecile , Massazza Gabriella , Destro Annarita , Bonzheim Irina , Rau Achim , Battmann Achim , Kah Bettina , Watkin Emmanuel , Hummel Michael
Published: January 2023

Accurate testing for epidermal growth factor receptor (EGFR) variants is essential for informing treatment decisions in non-small cell lung cancer (NSCLC). Automated diagnostic workflows may allow more streamlined initiation of targeted treatments, where appropriate, while comprehensive variant analysis is ongoing. FACILITATE, a real-world, prospective, multicenter, European study, evaluated performance and analytical turnaround time of the Idylla™ EGFR Mutation Test compared with local reference methods. Sixteen sites obtained formalin-fixed paraffin-embedded biopsy samples with ≥ 10% neoplastic cells from patients with NSCLC. Consecutive 5 μm sections from patient samples were tested for clinically relevant NSCLC-associated EGFR variants using the Idylla™ EGFR Mutation Test and local reference methods; performance (concordance) and analytical turnaround time were compared. Between January 2019 and November 2020, 1,474 parallel analyses were conducted. Overall percentage agreement was 97.7% [n = 1,418; 95% confidence interval (CI): 96.8–98.3], positive agreement, 87.4% (n = 182; 95% CI: 81.8–91.4) and negative agreement, 99.2% (n = 1,236; 95% CI: 98.5–99.6). There were 38 (2.6%) discordant cases. Ninety percent of results were returned with an analytical turnaround time of within 1 week using the Idylla™ EGFR Mutation Test versus ∼22 days using reference methods. The Idylla™ EGFR Mutation Test performed well versus local methods and had shorter analytical turnaround time. The Idylla™ EGFR Mutation Test can thus support application of personalized medicine in NSCLC.
Quality of life in older adults with mild cognitive impairment
Authors: Khan Fizah Mahnoor , Fatima Maryam , Qasim Syeda Maria , Khan Javeria Tahir , Saeed Aruba , Shamsi Rafia Farrukh
Published: January 2023

Background: Mild cognitive impairment (MCI) is a common phenomenon which is noticeably common among the older individuals population. Progression of this disorder is known to increase risk of Alzheimer's disease and Dementia. Objective: The objective of this study was to determine the association of quality of life and mild cognitive impairment in geriatric population. Methods: The data was collected using Memory Symptom Assessment Scale-Short Form (MSAS-SF) and Quality of life- Alzheimer Disease (QOL-AD) during a time period of six months from 300 individuals aged between 55-85years. The data analysis of this study was done using SPSS 21 version. Spearman test values were calculated to obtain results. Results: MSAD-SF and QOL-AD showed a significant decline of QOL in individuals with mild cognitive impairment. MSAS-SF and QOL-AD had a significant association with pain, lack of energy, difficulty sleeping, problems with urination, lack of appetite, dizziness, feeling sad, worrying, feeling irritable, memory, ability to do chores around the house, physical health, self as a whole and ability to do things for fun (pvalue< 0.05). Domains in both questionnaires indicated a decline in QOL with significant p-values of <0.05. Conclusion: In conclusion, those who had higher impairment level had lower quality of life in multiple domains.
Prevalence of research-related anxiety among students of Allied Health Sciences
Authors: Siddiqa Ayesha , Javed Hina , Khan Haseeb Muhammad , Michal Thomsina , Altaf Sana , Khan Usman
Published: January 2023

Background: Anxiety is one of the most common mental disorders. Although being detrimental, it is less researched upon than depression. While research is an essential component of medical education, it is also unfamiliar to undergraduate medical students. Therefore, research at the undergraduate level has been shown to cause anxiety among students. Objective: To determine research-related anxiety among allied Health Sciences students. Methods: A cross-sectional study was conducted in which a sample of 150 undergraduate students was selected on the basis of inclusion (no past history of mental illness, no traumatic incident in past 6 months and allied health sciences student from final year) and exclusion (traumatic incident in past 3 months, failure in recent major exam) criteria. The participants after signing the informed consent were recruited in the study through a non-probability convenient sampling technique. The data was collected using the Generalized Anxiety Disorder scale (GAD-7 scale). Data were analyzed through SPSS version 21. Results: In this study, 150 undergraduate students participated in the study. Results showed that out of the 150 students, 90 (60%) had mild anxiety related to research, 32(21%) students had moderate-level anxiety, and 28(18%) students had severe anxiety. Conclusion: According to the results of this study, the majority of students in their final year or semester experienced mild levels of research related-anxiety.
Sublingual Dermoid Cyst in Young Child
Authors: Hamada Masakazu , Okawa Rena , Masuda Katsuhiko , Tojo Fumikazu , Suehiro Yuto , Ogaya Yuko , Kinosada Hiroko , Uzawa Narikazu , Nakano Kazuhiko
Published: January 2023

A dermoid cyst is a benign congenital lesion of ectodermal origin that can arise in any region of the body, though occurrence is rare. A young girl aged 2 years 4 months was referred to our hospital because of a painless mass in the floor of the mouth. Intraoral examination findings revealed a painless movable elastic soft mass on the floor of the mouth measuring approximately 15 mm in diameter. Magnetic resonance imaging indicated a cystic lesion, with low signal intensity shown in T1-weighted and extremely high signal intensity in T2-weighted images. These clinical findings indicated the presence of a dermoid cyst and removal was planned. Under general anesthesia with nasal intubation, surgical removal was performed through an incision on the floor of the mouth. Blunt dissection exposed the integrity of the cyst capsule, which was weakly attached to adjacent tissue. The excised mass was 19 mm × 14 mm × 11 mm in size. Histological examination findings confirmed a diagnosis of dermoid cyst. The operation was successfully completed without any complications and the postoperative course was good. It is important to properly evaluate cysts in children and provide proper treatment with appropriate timing.
Corticosteroid Treatment in Sydenham Chorea: A 27-Year Tertiary Referral Center Experience
Authors: Cappellari Alberto Maria , Rogani Greta , Filocamo Giovanni , Petaccia Antonella
Published: January 2023

Objective: The purpose of this study was to investigate the effectiveness of corticosteroid therapy for children suffering from Sydenham chorea (SC). Methods: The design of the study was observational, retrospective and conducted at the single center of the Rheumatology Unit of Policlinic Hospital of Milan, Italy, from May 1995 to May 2022. All data about the patients were collected from medical records. Results: From a total of 59 patients enrolled in the study (44 females and 15 males; median age 9.3 years, range 7.4–10.6 years), 49 were eligible for primary outcome analysis (10 patients were excluded due to incomplete data). Overall, 75% of patients received steroid therapy, while the remaining cases were treated with symptomatic drugs, including neuroleptics and antiseizure drugs. We found that the duration of chorea was significantly shorter in patients treated with corticosteroids in comparison to those receiving symptomatic treatment (median time: 31 vs. 41 days, p = 0.023). Additionally, patients with arthritis at the onset of the disease had a longer duration of chorea than those without arthritis (median time 90.5 vs. 39 days, p = 0.02). We also found that chorea recurred in 12% of the patients and seemed to be linked to a younger age at onset (p = 0.01). Conclusions: The study suggests that corticosteroid therapy can lead to a faster resolution of SC when compared to neuroleptics and antiseizure drugs treatment.
Parental Feeding Practices and Children’s Eating Behaviours: An Overview of Their Complex Relationship
Authors: Costa Alexandra , Oliveira Andreia
Published: January 2023

Several studies have found an association between eating behaviours and weight status and obesity risk in childhood. Children’s eating behaviours arise from a combination of genetic and environmental factors. Parents appear to play a central role in their development as the main responsible for shaping children’s feeding environment and eating experiences. The purpose of this paper is to review the literature on parental influences on eating behaviours across childhood, mainly focusing on parental feeding practices. The associations between parental feeding practices and children’s eating behaviours have been extensively studied. However, most of the findings come from cross-sectional studies, so the possibility of reverse causality cannot be ruled out (i.e., children’s behaviours influencing parents). Most recently, a few longitudinal studies with a cross-lagged design have shown that the relationship between children’s eating behaviours and parental feeding practices seems to be bidirectional, where it is not straightforward whether parental feeding practices are a predictor or a consequence of children’s eating behaviours. Children’s eating behaviours influence parents to adopt certain feeding practices, but these practices also influence children’s behaviours over time. Parental feeding practices may have the potential to shape children’s eating behaviours and should be targeted to promote the development of non-obesogenic traits. However, parent–child interactions are complex and therefore both parent and child characteristics and the family dynamics should be considered.
Emotion Word Processing in Immersed Spanish-English/English-Spanish Bilinguals: An ERP Study
Authors: Cieślicka Anna B. , Guerrero Brenda L.
Published: January 2023

We conducted a lexical decision task to measure Spanish-English/English-Spanish bilinguals’ behavioral (RT) and electrophysiological (EPN, Early Posterior Negativity and LPC, Late Positive Complex) responses to English emotion words and their Spanish translation equivalents. Bilingual participants varied in age of acquisition (AoA of Spanish/English: early, late), language status (L1 Spanish, L1 English) and language dominance (English-dominant, Spanish-dominant, balanced) but were all highly immersed bicultural individuals, uniformly more proficient in English than Spanish. Behavioral data showed faster and more accurate responses to English than Spanish targets; however, the emotion effect was only present for Spanish, with positive Spanish words recognized significantly faster than those that were negative or neutral. In the electrophysiological data, the emotion response was affected by language of the target stimulus, with English targets eliciting larger EPN amplitudes than Spanish targets. The reverse effect was found on the LPC component, where Spanish targets elicited a higher positivity than English targets. Dominance did not turn out to be a significant predictor of bilingual performance. Results point to the relevance of proficiency in modulating bilingual lexical processing and carry implications for experimental design when examining immersed bilinguals residing in codeswitching environments.
Integrated Serum Metabolome and Gut Microbiome to Decipher Chicken Amino Acid Improvements Induced by Medium-Chain Monoglycerides
Authors: Liu Tao , Ruan Shengyue , Mo Qiufen , Zhao Minjie , Wang Jing , Ye Zhangying , Chen Li , Feng Fengqin
Published: January 2023

Chicken muscle yield and amino acid composition improvements with medium-chain monoglyceride (MG) supplementation were reported by previous studies, but the underlying mechanism was uncertain. This study aimed to decipher chicken amino acid improvements induced by medium-chain monoglycerides in the views of metabolomics, gene expression, and the gut microbiome. Newly hatched chicks (12,000 chicks) were weighed and randomly divided into two flocks, each with six replicates (1000 chicks per replicate), and fed a basal diet (the control group, CON) or a basal diet enriched with 300 mg/kg MG (the treated group, MG). Results demonstrated that MGs significantly increased the chicken flavor and essential and total amino acids. The serum amino acids and derivatives (betaine, l-leucine, l-glutamine, 1-methylhistide), as well as amino acid metabolism pathways in chickens, were enhanced by MG supplementation. Gene expression analysis exhibited that dietary MGs could improve muscle protein synthesis and cell growth via the mTOR/S6K1 pathway. Dietary MGs enhanced the cecal amino acid metabolism by selectively increasing the proportion of genera Lachnospiraceae_NK4A136_group and Bacteroides. Conclusively, the present study demonstrated that dietary MGs improved chicken amino acid composition via increasing both gut amino acid utilization and muscle amino acid deposition.
Integrating Metabolomics and Gene Expression Underlying Potential Biomarkers Compounds Associated with Antioxidant Activity in Southern Grape Seeds
Authors: Darwish Ahmed G. , Moniruzzaman Md , Tsolova Violeta , El-Sharkawy Islam
Published: January 2023

Different southern grape (Muscadine) genotypes (Muscadinia rotundifolia Michx.) were evaluated for their contents of metabolites in ripe berries. The metabolome study identified 331 metabolites in ripening skin and seed tissues. The major chemical groups were organic acids, fatty acyls, polyketides, and organic heterocycle compounds. The metabolic pathways of the identified metabolite were mainly arginine biosynthesis, D-glutamine, D-glutamate metabolism, alanine, aspartate metabolism, aminoacyl-tRNA biosynthesis, and citrate cycle. Principal component analysis indicated that catechin, gallic acid, and epicatechin-3-gallate were the main metabolites existing in muscadine seed extracts. However, citramalic and malic acids were the main metabolites contributing to muscadine skin extracts. Partial least-squares discriminant analysis (VIP > 1) described 25 key compounds indicating the metabolome in muscadine tissues (skin and seed). Correlation analysis among the 25 compounds and oxidation inhibition activities identified five biomarker compounds that were associated with antioxidant activity. Catechin, gallic acid, epicatechin-3-gallate, fertaric acid, and procyanidin B1 were highly associated with DPPH, FRAP, CUPRAC, and ABTS. The five biomarker compounds were significantly accumulated in the seed relative to the skin tissues. An evaluation of 15 antioxidant-related genes represented by the 3-dehydroquinate dehydratase (DHD), shikimate kinase (SK), chalcone synthase (CHS), anthocyanidin reductase (ANR), laccase (LAC), phenylalanine ammonia-lyase (PAL), dihydroflavonol 4-reductase (DFR), 3-dehydroquinate synthase (DHQS), chorismate mutase (CM), flavanone-3-hydroxylase (F3H), cinnamoyl-CoA reductase (CCR), cinnamyl alcohol dehydrogenase (CAD), leucoanthocyanidin reductase (LAR), gallate 1-β-glucosyltransferase (UGT), and anthocyanidin 3-O-glucosyltransferase (UFGT) encode critical enzymes related to polyphenolics pathway throughout four developmental stages (fruit-set FS, véraison V, ripe-skin R, and ripe-seed; S) in the C5 genotype demonstrated the dramatic accumulation of all transcripts in seed tissue or a developmental stage-dependent manner. Our findings suggested that muscadine grape seeds contain essential metabolites that could attract the attention of those interested in the pharmaceutical sector and the plant breeders to develop new varieties with high nutraceutical value.
Probiotics in Functional Dyspepsia
Authors: Tziatzios Georgios , Gkolfakis Paraskevas , Leite Gabriela , Mathur Ruchi , Damoraki Georgia , Giamarellos-Bourboulis Evangelos J. , Triantafyllou Konstantinos
Published: January 2023

Functional dyspepsia (FD) is a common disorder in everyday clinical practice identified nowadays as a multi-factorial, difficult to treat condition with a significant burden on patients’ quality of life (QoL) and healthcare systems worldwide. Despite its high prevalence in the general population, the precise etiology of the disorder remains elusive, with its pathophysiological spectrum evolving over time, including variable potential mechanisms, i.e., impaired gastric accommodation, gastric motor disorders, hypersensitivity to gastric distention, disorders of the brain–gut axis, as well as less evident ones, i.e., altered duodenal microbiota composition and genetic susceptibility. In light of these implications, a definitive, universal treatment that could be beneficial for all FD patients is not available yet. Recently, probiotics have been suggested to be an effective therapeutic option that could alleviate gastrointestinal symptoms in patients with Irritable Bowel Syndrome (IBS), potentially due to anti-inflammatory properties or by modulating the complex bidirectional interactions between gastrointestinal microbiota and host crosstalk; however, their impact on the multiple aspects of FD remains ambiguous. In this review, we aim to summarize all currently available evidence for the efficacy of probiotics as a novel therapeutic approach for FD.