bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constructing a prognostic model for head and neck squamous cell carcinoma based on glucose metabolism related genes
Authors: Liu Yu , Liu Nana , Zhou Xue , Zhao Lingqiong , Wei Wei , Hu Jie , Luo Zhibin 
Published: October 2023

BackgroundGlucose metabolism (GM) plays a crucial role in cancer cell proliferation, tumor growth, and survival. However, the identification of glucose metabolism-related genes (GMRGs) for effective prediction of prognosis in head and neck squamous cell carcinoma (HNSC) is still lacking.MethodsWe conducted differential analysis between HNSC and Normal groups to identify differentially expressed genes (DEGs). Key module genes were obtained using weighted gene co-expression network analysis (WGCNA). Intersection analysis of DEGs, GMRGs, and key module genes identified GMRG-DEGs. Univariate and multivariate Cox regression analyses were performed to screen prognostic-associated genes. Independent prognostic analysis of clinical traits and risk scores was implemented using Cox regression. Gene set enrichment analysis (GSEA) was used to explore functional pathways and genes between high- and low-risk groups. Immune infiltration analysis compared immune cells between the two groups in HNSC samples. Drug prediction was performed using the Genomics of Drug Sensitivity in Cancer (GDSC) database. Quantitative real-time fluorescence PCR (qRT-PCR) validated the expression levels of prognosis-related genes in HNSC patients.ResultsWe identified 4973 DEGs between HNSC and Normal samples. Key gene modules, represented by black and brown module genes, were identified. Intersection analysis revealed 76 GMRG-DEGs. Five prognosis-related genes (MTHFD2, CDKN2A, TPM2, MPZ, and DNMT1) were identified. A nomogram incorporating age, lymph node status (N), and risk score was constructed for survival prediction in HNSC patients. Immune infiltration analysis showed significant differences in five immune cell types (Macrophages M0, memory B cells, Monocytes, Macrophages M2, and Dendritic resting cells) between the high- and low-risk groups. GDSC database analysis identified 53 drugs with remarkable differences between the groups, including A.443654 and AG.014699. DNMT1 and MTHFD2 were up-regulated, while MPZ was down-regulated in HNSC.ConclusionOur study highlights the significant association of five prognosis-related genes (MTHFD2, CDKN2A, TPM2, MPZ, and DNMT1) with HNSC. These findings provide further evidence of the crucial role of GMRGs in HNSC.
“Forest is integral to life”: people-forest relations in the lower river region, the Gambia
Authors: Darboe Sarata , Manneh Lamin , Stryamets Nataliya , Prūse Baiba , Pieroni Andrea , Sõukand Renata , Mattalia Giulia 
Published: October 2023

IntroductionForests play a crucial role in the lives of millions of people worldwide by providing material and non-material contributions. Despite forests’ paramount importance from ecological, economic, and cultural perspectives, the long-term relationship between forests and local communities living in their proximity is often an undervalued contribution to our understanding of local ecological knowledge systems and forest changes.MethodsWe studied the interrelationships between the Mandinka peoples and forests in an understudied area of West Africa, the Gambia’s Lower River Region (LRR). Through 35 semi-structured interviews, we documented the forests’ contributions to local Mandinka peoples and their perception of forest changes. We also used geographic information systems (GIS software) for remote sensing satellite imagery to establish a baseline for these complex connections and changes.ResultsThis research revealed the crucial importance of the forest’s contributions to Mandinka communities and specifically to their psychological well-being. In addition, the interviewees revealed how ongoing socio-economic changes are affecting the human-forest relationship and possibly eroding the local ethnoforestry knowledge in the LRR of the Gambia. The most common forest contributions are those that provide material goods, serving as the driving force in connecting people with the forest, while non-material contributions are eroding due to complex socio-economic changes. Major socio-economic changes are also believed to drive the shift from dense forest to mixed forest and grassland.DiscussionIn line with the state of the art, the knowledge and perception of changes documented in this article underline the quintessential need to include local communities’ views in shaping forest management, in order to better fine-tune the strategies to safeguard biocultural diversity across forest areas.
Risk of head and neck cancer in relation to blood inflammatory biomarkers in the Swedish AMORIS cohort
Authors: Yang Yanping , Liang Yushan , Sadeghi Fatemeh , Feychting Maria , Hamar Niklas , Fang Fang , Zhang Zhe , Liu Qianwei 
Published: October 2023

BackgroundInflammation is critically involved in the development of human cancer, and blood inflammatory biomarkers have been proposed to indicate the risk of different cancer types.MethodsUsing the Swedish Apolipoprotein-Related Mortality Risk (AMORIS) Cohort (N=812,073), we first performed a time-to-event analysis to evaluate the association of the baseline level of 12 blood inflammatory biomarkers measured during 1985-1996 with the subsequent risk of head and neck cancer (HNC) identified through the nationwide Swedish Cancer Register until end of 2020. A nested case-control study was further conducted to demonstrate the longitudinal trends of the studied biomarkers during the 30-year period prior to diagnosis of HNC.ResultsIn the time-to-event analysis, we identified a total of 2,510 newly diagnosed HNC cases. There was an increased risk of HNC per standard deviation (SD) increase of haptoglobin (hazard ratio [HR]: 1.25; 95% confidence interval [CI]: 1.21-1.30), leukocytes (HR: 1.22; 95%CI: 1.17-1.28), sedimentation rate (HR: 1.17; 95%CI: 1.07-1.29), and monocytes (HR: 1.34; 95%CI: 1.07-1.68) at baseline, after adjustment for age, sex, fasting status, occupational status, and country of birth. In contrast, there was a decreased risk of HNC per SD increase of lymphocytes in % (HR: 0.85; 95%CI: 0.73-0.99) and lymphocyte-to-monocyte ratio (LMR) (HR: 0.81; 95%CI: 0.69-0.95) at baseline. In the nested case-control study using repeatedly measured biomarker levels, we found that individuals with HNC had consistently higher levels of haptoglobin, leukocytes, sedimentation rate, and monocytes, as well as consistently lower levels of lymphocytes in % and LMR, during the 30-year period prior to diagnosis, compared to controls.ConclusionBased on a cohort of more than half a million participants with up to 35 years of follow-up, our findings provide solid evidence supporting the presence of alterations in blood inflammatory biomarkers during the decades before diagnosis of HNC.
Beta-1,4-galactosyltransferase-3 deficiency suppresses the growth of immunogenic tumors in mice
Authors: Wei Heng , Naruse Chie , Takakura Daisuke , Sugihara Kazushi , Pan Xuchi , Ikeda Aki , Kawasaki Nana , Asano Masahide 
Published: October 2023

BackgroundBeta-1,4-galactosyltransferase-3 (B4GALT3) belongs to the family of beta-1,4-galactosyltransferases (B4GALTs) and is responsible for the transfer of UDP-galactose to terminal N-acetylglucosamine. B4GALT3 is differentially expressed in tumors and adjacent normal tissues, and is correlated with clinical prognosis in several cancers, including neuroblastoma, cervical cancer, and bladder cancer. However, the exact role of B4GALT3 in the tumor immune microenvironment (TIME) remains unclear. Here, we aimed to elucidate the function of B4GALT3 in the TIME.MethodsTo study the functions of B4GALT3 in cancer immunity, either weakly or strongly immunogenic tumor cells were subcutaneously transplanted into wild-type (WT) and B4galt3 knockout (KO) mice. Bone marrow transplantation and CD8+ T cell depletion experiments were conducted to elucidate the role of immune cells in suppressing tumor growth in B4galt3 KO mice. The cell types and gene expression in the tumor region and infiltrating CD8+ T cells were analyzed using flow cytometry and RNA sequencing. N-glycosylated proteins from WT and B4galt3 KO mice were compared using the liquid chromatography tandem mass spectrometry (LC-MS/MS)-based glycoproteomic approach.ResultsB4galt3 KO mice exhibited suppressed growth of strongly immunogenic tumors with a notable increase in CD8+ T cell infiltration within tumors. Notably, B4galt3 deficiency led to changes in N-glycan modification of several proteins, including integrin alpha L (ITGAL), involved in T cell activity and proliferation. In vitro experiments suggested that B4galt3 KO CD8+ T cells were more susceptible to activation and displayed increased downstream phosphorylation of FAK linked to ITGAL.ConclusionOur study demonstrates that B4galt3 deficiency can potentially boost anti-tumor immune responses, largely through enhancing the influx of CD8+ T cells. B4GALT3 might be suppressing cancer immunity by synthesizing the glycan structure of molecules on the CD8+ T cell surface, as evidenced by the changes in the glycan structure of ITGAL in immune cells. Importantly, B4galt3 KO mice showed no adverse effects on growth, development, or reproduction, underscoring the potential of B4GALT3 as a promising and safe therapeutic target for cancer treatment.
Functional genetic variation in pe/ppe genes contributes to diversity in Mycobacterium tuberculosis lineages and potential interactions with the human host
Authors: Gómez-González Paula Josefina , Grabowska Anna D. , Tientcheu Leopold D. , Tsolaki Anthony G. , Hibberd Martin L. , Campino Susana , Phelan Jody E. , Clark Taane G. 
Published: October 2023

IntroductionAround 10% of the coding potential of Mycobacterium tuberculosisis constituted by two poorly understood gene families, the pe and ppe loci, thought to be involved in host-pathogen interactions. Their repetitive nature and high GC content have hindered sequence analysis, leading to exclusion from whole-genome studies. Understanding the genetic diversity of pe/ppe families is essential to facilitate their potential translation into tools for tuberculosis prevention and treatment.MethodsTo investigate the genetic diversity of the 169 pe/ppe genes, we performed a sequence analysis across 73 long-read assemblies representing seven different lineages of M. tuberculosis and M. bovis BCG. Individual pe/ppe gene alignments were extracted and diversity and conservation across the different lineages studied.ResultsThe pe/ppe genes were classified into three groups based on the level of protein sequence conservation relative to H37Rv, finding that &gt;50% were conserved, with indels in pe_pgrs and ppe_mptr sub-families being major drivers of structural variation. Gene rearrangements, such as duplications and gene fusions, were observed between pe and pe_pgrs genes. Inter-lineage diversity revealed lineage-specific SNPs and indels.DiscussionThe high level of pe/ppe genes conservation, together with the lineage-specific findings, suggest their phylogenetic informativeness. However, structural variants and gene rearrangements differing from the reference were also identified, with potential implications for pathogenicity. Overall, improving our knowledge of these complex gene families may have insights into pathogenicity and inform the development of much-needed tools for tuberculosis control.
Bioinformatics and system biology approach to identify the influences of SARS-CoV-2 on metabolic unhealthy obese patients
Authors: Huang Tengda , Jiang Nan , Song Yujia , Pan Hongyuan , Du Ao , Yu Bingxuan , Li Xiaoquan , He Jinyi , Yuan Kefei , Wang Zhen 
Published: October 2023

Introduction: The severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) has posed a significant challenge to individuals’ health. Increasing evidence shows that patients with metabolic unhealthy obesity (MUO) and COVID-19 have severer complications and higher mortality rate. However, the molecular mechanisms underlying the association between MUO and COVID-19 are poorly understood.Methods: We sought to reveal the relationship between MUO and COVID-19 using bioinformatics and systems biology analysis approaches. Here, two datasets (GSE196822 and GSE152991) were employed to extract differentially expressed genes (DEGs) to identify common hub genes, shared pathways, transcriptional regulatory networks, gene-disease relationship and candidate drugs.Results: Based on the identified 65 common DEGs, the complement-related pathways and neutrophil degranulation-related functions are found to be mainly affected. The hub genes, which included SPI1, CD163, C1QB, SIGLEC1, C1QA, ITGAM, CD14, FCGR1A, VSIG4 and C1QC, were identified. From the interaction network analysis, 65 transcription factors (TFs) were found to be the regulatory signals. Some infections, inflammation and liver diseases were found to be most coordinated with the hub genes. Importantly, Paricalcitol, 3,3′,4,4′,5-Pentachlorobiphenyl, PD 98059, Medroxyprogesterone acetate, Dexamethasone and Tretinoin HL60 UP have shown possibility as therapeutic agents against COVID-19 and MUO.Conclusion: This study provides new clues and references to treat both COVID-19 and MUO.
Predicting food waste in households with children: socio-economic and food-related behavior factors
Authors: Tonini Pietro , Odina Pere Muñoz , Durany Xavier Gabarrell 
Published: October 2023

IntroductionThe consumption phase accounts for approximately half of the food waste generated within the food system. Numerous studies have identified families with children as the primary contributors to food waste. The aims of this paper is to enhance the comprehension of food waste behaviors in households with children by characterizing it and studying how socioeconomic characteristics and food-related behaviors can predict it.MethodsA survey was conducted among 806 families with children, categorized by the child’s age and family structure. The study utilized descriptive statistics to summarize the food waste behaviors and binary regression to evaluate the predictive abilities of 12 variable related to the socio-economic characteristic, purchase, and preparation behaviors and diet quality factors.ResultsPerishable food items, such as fruits, vegetables, cereal-based product, and dairy products, were the primary items wasted in households with children. Two patterns of food waste were identified: inadequate food management leading to small amounts of waste in families with young and middle-aged children, and over-purchasing perishable items leading to waste in other households with children. Household type and purchasing habits were significant predictors, while the purchaser’s age and buying channel showed lower predictive capacity.DiscussionPolicies to reduce food waste should prioritize raising awareness among children, promoting good practices at the household level, and creating favorable conditions during purchases. Strategies include enlisting children’s participation in meal planning and food preparation as well as limiting the promotion of ultra-processed products and incentivizing the sale of bulk products at supermarket.
MRI for the detection of small malignant renal masses: a systematic review and meta-analysis
Authors: Shang Wenwen , Hong Guohui , Li Wei 
Published: October 2023

ObjectiveWe aimed to review the available evidence on the diagnostic performance of magnetic resonance imaging in differentiating malignant from benign small renal masses.MethodsAn electronic literature search of Web of Science, MEDLINE (Ovid and PubMed), Cochrane Library, EMBASE, and Google Scholar was performed to identify relevant articles up to 31 January 2023. We included studies that reported the diagnostic accuracy of using magnetic resonance imaging to differentiate small (≤4 cm) malignant from benign renal masses. The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, and diagnostic odds ratio were calculated using the bivariate model and the hierarchical summary receiver operating characteristic model. The study quality evaluation was performed with the Quality Assessment of Diagnostic Accuracy Studies-2 tool.ResultsA total of 10 studies with 860 small renal masses (815 patients) were included in the current meta-analysis. The pooled sensitivity and specificity of the studies for the detection of malignant masses were 0.85 (95% CI 0.79-0.90) and 0.83 (95% CI 0.67-0.92), respectively.ConclusionsMRI had a moderate diagnostic performance in differentiating small malignant renal masses from benign ones. Substantial heterogeneity was observed between studies for both sensitivity and specificity.
Abdominal lymph node metastasis in non-surgical esophageal squamous cell carcinoma: prognostic significance and a novel staging strategy
Authors: Zhao Zongxing , Wang Hongmin , Liu Yajing , Li Minghuan , Li Mingjun 
Published: October 2023

PurposeThis study aimed to evaluate the feasibility of a combination of abdominal lymph node (LN) metastasis and the number of LNs in esophageal squamous cell carcinoma (ESCC) patients to optimize its clinical nodal staging.MethodsA retrospective study, including a total of 707 ESCC patients treated with definitive radiotherapy, was conducted at two participating institutes. Different combinations of LN variables, including abdominal LN metastasis (R1: no-abdominal LN metastasis; R2: abdominal LN metastasis), were further analyzed to propose a potential revised nodal (rN) staging.ResultsThe multivariate analyses showed that the number of metastatic LN and abdominal LN metastasis were independent prognostic factors for the overall survival (OS). The results showed no significant differences in the OS between the N2 patients with abdominal LN metastasis and N3 patients. The OS of the stage III patients with abdominal LN metastasis was not significantly different from those with stage IVa. The N3R1 and N1-2R2 had similar hazard ratios (HRs). The N1R1 subset was defined as rN1, the N2R1 subset was defined as rN2, and the N3R1-2 and N1-2R2 subsets were defined as rN3. The HRs of OS of the rN2 and rN3 groups increased subsequently. The rN stage could identify the differences in the OS times of each subgroup based on the 8th AJCC cN staging or the 11th JES N staging.ConclusionsThe rN staging, including the number of metastatic LNs and abdominal LN metastasis, might serve as a potential prognostic predictor for non-surgical patients with ESCC.
Respiratory patterns in spontaneously breathing near-term lambs delivered by caesarean section under spinal anaesthesia
Authors: Davies I. M. , Crossley K. J. , McGillick E. V. , Nitsos I. , Rodgers K. , Thiel A. , Zahra V. A. , te Pas A. B. , Hooper S. B. 
Published: October 2023

IntroductionThe transition to newborn life has typically been studied in intubated and mechanically ventilated newborn lambs delivered via caesarean section (CS) under general anaesthesia. As a result, little is known of the spontaneous breathing patterns in lambs at birth, particularly those at risk of developing respiratory distress (RD). We have developed a method for delivering spontaneously breathing near-term lambs to characterise their breathing patterns in the immediate newborn period.MethodsAt 137–8 days gestation (2–3 days prior to delivery; term ∼147 days), fetal lambs (n = 7) were partially exteriorised for instrumentation (insertion of catheters and flow probes) before they were returned to the uterus. At 140 days, lambs were delivered via CS under light maternal sedation and spinal anaesthesia. Lambs were physically stimulated and when continuous breathing was established, the umbilical cord was clamped. Breathing patterns were assessed by measuring intrapleural and upper-tracheal pressures during the first four hours after birth.ResultsNewborn lambs display significant heterogeneity in respiratory patterns in the immediate newborn period that change with time after birth. Seven distinct breathing patterns were identified including: (i) quiet (tidal) breathing, (ii) breathing during active periods, (iii) breathing during oral feeding, (iv) tachypnoea, (v) expiratory braking manoeuvres, (vi) expiratory pauses or holding, and (vii) step changes in ventilation.ConclusionsWe have described normal respiratory behaviour in newborn lambs, in order to identify respiratory behaviours that are indicative of RD in term newborn infants.
Effects of gamma radiation on engineered tomato biofortified for space agriculture by morphometry and fluorescence-based indices
Authors: Pagliarello Riccardo , Bennici Elisabetta , Di Sarcina Ilaria , Villani Maria Elena , Desiderio Angiola , Nardi Luca , Benvenuto Eugenio , Cemmi Alessia , Massa Silvia 
Published: October 2023

IntroductionFuture long-term space missions will focus to the solar system exploration, with the Moon and Mars as leading goals. Plant cultivation will provide fresh food as a healthy supplement to astronauts’ diet in confined and unhealthy outposts. Ionizing radiation (IR) are a main hazard in outer space for their capacity to generate oxidative stress and DNA damage. IR is a crucial issue not only for human survival, but also for plant development and related value-added fresh food harvest. To this end, efforts to figure out how biofortification of plants with antioxidant metabolites (such as anthocyanins) may contribute to improve their performances in space outposts are needed.MethodsMicroTom plants genetically engineered to express the Petunia hybrida PhAN4 gene, restoring the biosynthesis of anthocyanins in tomato, were used. Seeds and plants from wild type and engineered lines AN4-M and AN4-P2 were exposed to IR doses that they may experience during a long-term space mission, simulated through the administration of gamma radiation. Plant response was continuously evaluated along life cycle by a non-disturbing/non-destructive monitoring of biometric and multiparametric fluorescence-based indices at both phenotypic and phenological levels, and indirectly measuring changes occurring at the primary and secondary metabolism level.ResultsResponses to gamma radiation were influenced by the phenological stage, dose and genotype. Wild type and engineered plants did not complete a seed-to-seed cycle under the exceptional condition of 30 Gy absorbed dose, but were able to cope with 0.5 and 5 Gy producing fruits and vital seeds. In particular, the AN4-M seeds and plants showed advantages over wild type: negligible variation of fluorimetric parameters related to primary metabolism, no alteration or improvement of yield traits at maturity while maintaining smaller habitus than wild type, biosynthesis of anthocyanins and maintained levels of these compounds compared to non-irradiated controls of the same age.DiscussionThese findings may be useful in understanding phenotypic effects of IR on plant growth in space, and lead to the exploitation of new breeding efforts to optimize plant performances to develop appropriate ideotypes for future long-term space exploration extending the potential of plants to serve as high-value product source.