bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative Human Paleogenetics: What can Ancient DNA Tell us About Complex Trait Evolution?
Authors: Irving-Pease Evan K. , Muktupavela Rasa , Dannemann Michael , Racimo Fernando
Published: August 2021

Genetic association data from national biobanks and large-scale association studies have provided new prospects for understanding the genetic evolution of complex traits and diseases in humans. In turn, genomes from ancient human archaeological remains are now easier than ever to obtain, and provide a direct window into changes in frequencies of trait-associated alleles in the past. This has generated a new wave of studies aiming to analyse the genetic component of traits in historic and prehistoric times using ancient DNA, and to determine whether any such traits were subject to natural selection. In humans, however, issues about the portability and robustness of complex trait inference across different populations are particularly concerning when predictions are extended to individuals that died thousands of years ago, and for which little, if any, phenotypic validation is possible. In this review, we discuss the advantages of incorporating ancient genomes into studies of trait-associated variants, the need for models that can better accommodate ancient genomes into quantitative genetic frameworks, and the existing limits to inferences about complex trait evolution, particularly with respect to past populations.
Host Genetics of Response to Porcine Reproductive and Respiratory Syndrome in Sows: Reproductive Performance
Authors: Hickmann Felipe M. W. , Braccini Neto José , Kramer Luke M. , Huang Yijian , Gray Kent A. , Dekkers Jack C. M. , Sanglard Leticia P. , Serão Nick V. L.
Published: August 2021

Porcine Reproductive and Respiratory Syndrome (PRRS) is historically the most economically important swine disease worldwide that severely affects the reproductive performance of sows. However, little is still known about the genetic basis of reproductive performance in purebred herds during a PRRS outbreak through the comparison of maternal and terminal breeds. Thus, the objective of this work was to explore the host genetics of response to PRRS in purebred sows from two breeds. Reproductive data included 2546 Duroc and 2522 Landrace litters from 894 and 813 purebred sows, respectively, which had high-density genotype data available (29,799 single nucleotide polymorphisms; SNPs). The data were split into pre-PRRS, PRRS, and post-PRRS phases based on standardized farrow-year-week estimates. Heritability estimates for reproductive traits were low to moderate (≤0.20) for Duroc and Landrace across PRRS phases. On the other hand, genetic correlations of reproductive traits between PRRS phases were overall moderate to high for both breeds. Several associations between MARC0034894, a candidate SNP for response to PRRS, with reproductive performance were identified (P-value < 0.05). Genomic analyses detected few QTL for reproductive performance across all phases, most explaining a small percentage of the additive genetic variance (≤8.2%, averaging 2.1%), indicating that these traits are highly polygenic. None of the identified QTL within a breed and trait overlapped between PRRS phases. Overall, our results indicate that Duroc sows are phenotypically more resilient to PRRS than Landrace sows, with a similar return to PRRS-free performance between breeds for most reproductive traits. Genomic prediction results indicate that genomic selection for improved reproductive performance under a PRRS outbreak is possible, especially in Landrace sows, by training markers using data from PRRS-challenged sows. On the other hand, the high genetic correlations with reproductive traits between PRRS phases suggest that selection for improved reproductive performance in a clean environment could improve performance during PRRS, but with limited efficiency due to their low heritability estimates. Thus, we hypothesize that an indicator trait that could be indirectly selected to increase the response to selection for these traits would be desirable and would also improve the reproductive performance of sows during a PRRS outbreak.
Gene Set Enrichment Analysis Reveals Individual Variability in Host Responses in Tuberculosis Patients
Authors: Domaszewska Teresa , Zyla Joanna , Otto Raik , Kaufmann Stefan H. E. , Weiner January
Published: August 2021

Group-aggregated responses to tuberculosis (TB) have been well characterized on a molecular level. However, human beings differ and individual responses to infection vary. We have combined a novel approach to individual gene set analysis (GSA) with the clustering of transcriptomic profiles of TB patients from seven datasets in order to identify individual molecular endotypes of transcriptomic responses to TB. We found that TB patients differ with respect to the intensity of their hallmark interferon (IFN) responses, but they also show variability in their complement system, metabolic responses and multiple other pathways. This variability cannot be sufficiently explained with covariates such as gender or age, and the molecular endotypes are found across studies and populations. Using datasets from a Cynomolgus macaque model of TB, we revealed that transcriptional signatures of different molecular TB endotypes did not depend on TB progression post-infection. Moreover, we provide evidence that patients with molecular endotypes characterized by high levels of IFN responses (IFN-rich), suffered from more severe lung pathology than those with lower levels of IFN responses (IFN-low). Harnessing machine learning (ML) models, we derived gene signatures classifying IFN-rich and IFN-low TB endotypes and revealed that the IFN-low signature allowed slightly more reliable overall classification of TB patients from non-TB patients than the IFN-rich one. Using the paradigm of molecular endotypes and the ML-based predictions allows more precisely tailored treatment regimens, predicting treatment-outcome with higher accuracy and therefore bridging the gap between conventional treatment and precision medicine.
Replication/Assembly Defective Avian Flavivirus With Internal Deletions in the Capsid Can Be Used as an Approach for Living Attenuated Vaccine
Authors: He Yu , Wang Xiaoli , Guo Jiaqi , Mao Li , Zhang Senzhao , Hu Tao , Wang Mingshu , Jia Renyong , Zhu Dekang , Liu Mafeng , Zhao Xinxin , Yang Qiao , Wu Ying , Zhang Shaqiu , Huang Juan , Mao Sai , Ou Xumin , Gao Qun , Sun Di , Liu Yunya , Zhang Ling , Yu Yanling , Cheng Anchun , Chen Shun
Published: August 2021

Avian Tembusu virus (TMUV) is a novel flavivirus causing severe egg drop and fatal encephalitis in avian in Asia. In the present study, we screened the structural and functional requirements of TMUV capsid protein (CP) for viral morphogenesis using reverse genetics methods in combination with replicon packaging assays. TMUV-CP showed dramatic functional and structural flexibility, and even though 44 residues were removed from the N-terminus, it was still capable of packaging replicon RNA; in addition, 33 residues were deleted from the C-terminus (containing nearly the entire α4-helix), and infectious particles were still produced, although α4-α4’ is supposedly vital for CP dimerization and nucleocapsid formation. We further analyzed two mutants (ΔC20-43 and ΔC64-96 viruses) with relatively large deletions that still replicated well in BHK-21 cells. Our data indicate that internal deletions within CP impaired viral replication or assembly, resulting in attenuated virus proliferation in cells and attenuated virulence in duck embryos, and these deletion mutations are quite stable in cell culture. An in vivo assay indicated that both ΔC20-43 virus and ΔC64-96 virus were highly attenuated in ducklings but still immunogenic. Single-dose immunization with ΔC20-43 virus or ΔC64-96 virus could protect ducklings from a lethal challenge with good antigen clearance. Together, our data shed light on replication/assembly defective TMUV with internal deletions in CP and provide an effective approach to attenuate viral virulence in live vaccines without changing the antigen composition.
ULK1 Inhibition as a Targeted Therapeutic Strategy for Psoriasis by Regulating Keratinocytes and Their Crosstalk With Neutrophils
Authors: Qiu Xiaonan , Zheng Lin , Liu Xiuting , Hong Dan , He Mintong , Tang Zengqi , Tian Cuicui , Tan Guozhen , Hwang Sam , Shi Zhenrui , Wang Liangchun
Published: August 2021

Psoriasis is a common inflammatory skin disease resulting from an interplay of keratinocytes and immune cells. Previous studies have identified an essential role of autophagy in the maintenance of epidermal homeostasis including proliferation and differentiation. However, much less is known about the role of autophagy-related proteins in the cutaneous immune response. Herein, we showed that ULK1, the key autophagic initiator, and its phosphorylation at Ser556 were distinctively decreased in the epidermis from lesional skin of psoriasis patients. Topical application of SBI0206965, a selective ULK1 inhibitor, significantly attenuated epidermal hyperplasia, infiltration of neutrophils, and transcripts of the psoriasis-related markers in imiquimod (IMQ)-induced psoriasiform dermatitis (PsD). In vitro, ULK1 impairment by siRNA and SBI0206965 arrested cell proliferation and promoted apoptosis of keratinocytes but had a marginal effect on the expression of proinflammatory mediators under steady status. Surprisingly, SBI0206965 blocked the production of chemokines and cytokines in keratinocytes stimulated by neutrophils. Of interest, the pro-apoptotic and anti-inflammatory effects of ULK1 inhibition cannot be fully replicated by autophagic inhibitors. Our findings suggest a self-regulatory process by downregulating ULK1 to maintain the immune homeostasis of psoriatic skin via regulating keratinocytes and their crosstalk with neutrophils, possibly through both autophagy-dependent and independent mechanisms. ULK1 might be a potential target for preventing or treating psoriasis.
PADI2 Polymorphisms Are Significantly Associated With Rheumatoid Arthritis, Autoantibodies Serologic Status and Joint Damage in Women from Southern Mexico
Authors: Guzmán-Guzmán Iris Paola , Ramírez-Vélez Claudia Isabel , Falfán-Valencia Ramcés , Navarro-Zarza José Eduardo , Gutiérrez-Pérez Ilse Adriana , Zaragoza-García Oscar , Ramírez Mónica , Castro-Alarcón Natividad , Parra-Rojas Isela
Published: August 2021

The enzymes of the family peptidylarginine deiminases (PADs) have an important role in the pathogenesis of rheumatoid arthritis (RA) due to their association with the anti-citrullinated protein antibodies (ACPA) production. To evaluate the association between single-nucleotide polymorphisms (SNPs) in the PADI2 gene and RA susceptibility, related clinical parameters, and the serologic status of autoantibodies in a women population with RA from southern Mexico, a case-control study was conducted (case n=229; control n=333). Sociodemographic characteristics were evaluated, along with clinical parameters, inflammation markers, the levels of ACPAs as anti-cyclic citrullinated peptides (anti-CCPs), anti-modified citrullinated vimentin (anti-MCV), and rheumatoid factor (RF). Genomic DNA was extracted from peripheral blood, and three SNPs of the PADI2 gene (rs1005753, rs2057094, and rs2235926) were performed by qPCR using TaqMan probes. The data analysis reveals that the carriers of the T allele for rs2057094 and rs2235926 presented an earlier onset of the disease (β= -3.26; p = 0.03 and β = -4.13; p = 0.015, respectively) while the carriers of the T allele for rs1005753 presented higher levels of anti-CCPs (β= 68.3; p = 0.015). Additionally, the T allele of rs2235926 was associated with a positive RF (OR = 2.90; p = 0.04), anti-MCV (OR = 2.92; p = 0.05), and with the serologic status anti-CCP+/anti-MCV+ (OR = 3.02; p = 0.03), and anti-CCP+/anti-MCV+/RF+ (OR = 3.79; p = 0.004). The haplotypes GTT (OR =1.52; p = 0.027) and TTT (OR = 1.32; p = 0.025) were associated with the presence of RA. In addition, in this study the haplotype TTT is linked to the presence of radiographic joint damage defined by a Sharp-van der Heijde score (SHS) ≥2 (OR = 1.97; p = 0.0021) and SHS ≥3 (OR = 1.94; p = 0.011). The haplotype TTT of SNPs rs1005753, rs2057094, and rs2235926 of the PADI2 gene confers genetic susceptibility to RA and radiographic joint damage in women from southern Mexico. The evidence reveals that SNPs of the PADI2 gene favors the presence of a positive serologic status in multiple autoantibodies and the clinical manifestations of RA at an early onset age.
Modelling the Distribution of a Commercial NE-Atlantic Sea Cucumber, Holothuria mammata: Demographic and Abundance Spatio-Temporal Patterns
Authors: Félix Pedro M. , Pombo Ana , Azevedo e Silva Francisco , Simões Tomás , Marques Tiago A. , Melo Ricardo , Rocha Cristina , Sousa João , Venâncio Eliana , Costa José L. , Brito Ana C.
Published: August 2021

There is an increasing demand for sea cucumbers, for human consumption, mainly from Asian markets and, as a consequence, NE-Atlantic species are now new targets for exploitation and exportation. Holothuria mammata is one of the most valuable species in Europe. However, the lack of historical economic interest in this species in most European countries has also led to a lack of studies concerning biological and ecological aspects on wild populations and this is a major issue for stock management. This study aims to determine the temporal and spatial patterns of distribution of H. mammata, considering its abundance and demographic structure in a NE-Atlantic area, SW Portugal, as a function of environmental conditions. For that, a population from a marine protected area was followed for 1 year at 1.5-month intervals. Throughout the coastal area, six sites were selected and at each sampling campaign three random transects per site and substrate (rock and sand) in which all H. mammata individuals were counted and measured. For each site and survey several environmental parameters of interest, from the water column, the sediment and substrate cover, were also measured. Generalized Linear Models were used to model the spatial and temporal distribution of the species according to environmental conditions, to determine the species’ habitat preferences. The distribution models indicate that abiotic and biotic parameters of the water column are not the main drivers shaping the distribution of H. mammata. The species has a patchy distribution, and its habitat preferences depend on environmental stability, the presence of shelter and habitat complexity, which is more important for smaller, more vulnerable, individuals, while bigger size classes tend to venture more into less stable environments in an opportunistic fashion. The knowledge of these population traits is determinant to develop stock management measures, which are now urgent to prevent the depletion of commercial sea cucumber populations in the NE-Atlantic. Sustainable fisheries policies should be developed and start by considering to delimit fishing areas and periods, considering the species spatial and temporal distribution patterns.
Specific Features of the Coagulopathy Signature in Severe COVID-19 Pneumonia
Authors: Blot Mathieu , de Maistre Emmanuel , Bourredjem Abderrahmane , Quenot Jean-Pierre , Nguyen Maxime , Bouhemad Belaid , Charles Pierre-Emmanuel , Binquet Christine , Piroth Lionel
Published: August 2021

Rationale: COVID-19 displays distinct characteristics that suggest a unique pathogenesis. The objective of this study was to compare biomarkers of coagulopathy and outcomes in COVID-19 and non-COVID-19 patients with severe pneumonia.

Methods: Thirty-six non-COVID-19 and 27 COVID-19 non-immunocompromised patients with severe pneumonia were prospectively enrolled, most requiring intensive care. Clinical and biological characteristics (including plasma biomarkers of coagulopathy) were compared.

Results: At similar baseline severity, COVID-19 patients required mechanical ventilation (MV) for significantly longer than non-COVID-19 patients (p = 0.0049) and more frequently developed venous thrombotic complications (p = 0.031). COVID-19 patients had significantly higher plasma concentrations of soluble VCAM1 (sVCAM1) (5,739 ± 3,293 vs. 3,700 ± 2,124 ng/ml; p = 0.009), but lower levels of D-dimers, vWF-A2, sICAM1, sTREM1, VEGF, and P-selectin, compared to non-COVID-19 patients. Principal component analysis identified two main patterns, with a clear distinction between non-COVID-19 and COVID-19 patients. Multivariable regression analysis confirmed that sVCAM1 rising levels were independently associated with a longer duration of MV. Finally, we identified close correlations between sVCAM1 and some features of COVID-19 immune dysregulation (ie. CXCL10, GM-CSF, and IL-10).

Conclusion: We identified specific features of the coagulopathy signature in severe COVID-19 patients, with higher plasma sVCAM1 levels, that were independently associated with the longer duration of mechanical ventilation.

Clinical Trial Registration:ClinicalTrials.gov, identifier: NCT03505281.
External Validation of aMAP Hepatocellular Carcinoma Risk Score in Patients With Chronic Hepatitis B-Related Cirrhosis Receiving ETV or TDF Therapy
Authors: Gui Honglian , Huang Yan , Zhao Gangde , Chen Lichang , Cai Wei , Wang Hui , Guo Qing , Xie Qing
Published: August 2021

Background and Aim: A prediction model of hepatocellular carcinoma (HCC) risk in patients with chronic liver diseases, based on age, male sex, albumin-bilirubin, and platelets (aMAP), has been previously reported. We validated the aMAP score and compared its performance to those of other risk scores in an independent at-risk cohort.

Methods: Treatment-naïve patients with chronic hepatitis B-related compensated cirrhosis who received entecavir or tenofovir monotherapy for at least 12 months were enrolled in this study. The performances of the aMAP and other HCC risk scores were assessed using Harrell's c-index, and predefined cut-off values were evaluated using survival analysis.

Results: Of the 1,042 patients, 131 (12.6%) developed HCC during a median follow-up of 41 months. The aMAP score provided the highest Harrell's c-index (0.724), followed by CAMD (0.719), mPAGE-B (0.719), and PAGE-B (0.695). The 5-year cumulative HCC probabilities were 2.9% for patients with a low aMAP score (<50), 11.2% for patients with an intermediate aMAP score (50–60), and 27.9% for patients with a high aMAP score (>60). Using both aMAP and mPAGE-B, 11.6% of patients were identified as low risk with a negative predictive value of 98.2% for not developing HCC within 5 years. Patients with aMAP >60 and diabetes exhibited an extremely high risk of HCC, with a cumulative incidence of 49.3% at 5 years. The predictive performance of aMAP with a reassessment at 1 year after the initiation of antiviral therapy outperformed the predictive performance of aMAP at enrollment.

Conclusions: The aMAP score accurately predicted the risk of HCC in at-risk patients with compensated cirrhosis undergoing antiviral therapy. A combination of the aMAP score and diabetes status could further stratify the risk of HCC.
Taxonomy and Phylogeny of Four New Species in Absidia (Cunninghamellaceae, Mucorales) From China
Authors: Zong Tong-Kai , Zhao Heng , Liu Xiao-Ling , Ren Li-Ying , Zhao Chang-Lin , Liu Xiao-Yong
Published: August 2021

Four new species within the genus Absidia, A. globospora, A. medulla, A. turgida, and A. zonata, are proposed based on a combination of morphological traits, physiological features, and molecular evidences. A. globospora is characterized by globose sporangiospores, a 1.0- to 3.5-μm-long papillary projection on columellae, and sympodial sporangiophores. A. medulla is characterized by cylindrical to oval sporangiospores, a 1.0- to 4.5-μm-long bacilliform projection on columellae, and spine-like rhizoids. A. turgida is characterized by variable sporangiospores, up to 9.5-μm-long clavate projections on columellae, and swollen top of the projection and inflated hyphae. A. zonata is characterized by cylindrical to oval sporangiospores, a 2.0- to 3.5-μm-long spinous projection on columellae, and as many as eight whorled sporangiophores. Phylogenetic analyses based on sequences of internal transcribed spacer rDNA and D1–D2 domains of LSU rDNA support the novelty of these four species within the Absidia. All new species are illustrated, and an identification key to all the known species of Absidia in China is included.
Microbial Diversity and Metabolite Profile of Fermenting Millet in the Production of Hausa koko, a Ghanaian Fermented Cereal Porridge
Authors: Atter Amy , Diaz Maria , Tano-Debrah Kwaku , Kunadu Angela Parry-Hanson , Mayer Melinda J. , Colquhoun Ian J. , Nielsen Dennis Sandris , Baker David , Narbad Arjan , Amoa-Awua Wisdom
Published: August 2021

Hausa kokois an indigenous porridge processed from millet in Ghana. The process involves fermentation stages, giving the characteristic organoleptic properties of the product that is produced largely at a small-scale household level and sold as a street food. Like many other indigenous foods, quality control is problematic and depends on the skills of the processor. In order to improve the quality of the product and standardize the process for large-scale production, we need a deeper understanding of the microbial processes. The aim of this study is to investigate the microbial community involved in the production of this traditional millet porridge and the metabolites produced during processing. High-throughput amplicon sequencing was used to identify the bacterial (16S rRNA V4 hypervariable region) and fungal [Intergenic Transcribed Spacer (ITS)] communities associated with the fermentation, while nuclear magnetic resonance (NMR) was used for metabolite profiling. The bacterial community diversity was reduced during the fermentation processes with an increase and predominance of lactobacilli. Other dominant bacteria in the fermentation includedPediococcus,Weissella,Lactococcus,Streptococcus,Leuconostoc, andAcetobacter.The speciesLimosilactobacillus fermentumandLigilactobacillus salivariusaccounted for some of the diversities within and between fermentation time points and processors. The fungal community was dominated by the genusSaccharomyces. Other genera such asPichia,Candida,Kluyveromyces,Nakaseomyces,Torulaspora, andCyberlindnerawere also classified. The speciesSaccharomyces cerevisiae,Stachybotrys sansevieriae,Malassezia restricta,Cyberlindnera fabianii, andKluyveromyces marxianusaccounted for some of the diversities within some fermentation time points. The speciesS. sansevieriaandM. restrictamay have been reported for the first time in cereal fermentation. This is the most diverse microbial community reported inHausa koko. In this study, we could identify and quantify 33 key different metabolites produced by the interactions of the microbial communities with the millet, composed of organic compounds, sugars, amino acids and intermediary compounds, and other key fermentation compounds. An increase in the concentration of organic acids in parallel with the reduction of sugars occurred during the fermentation process while an initial increase of amino acids followed by a decrease in later fermentation steps was observed.
Dynamic Changes in Lung Microbiota of Broilers in Response to Aging and Ammonia Stress
Authors: Chen Jian , Jin Ai , Huang Lei , Zhao Yan , Li Yuwen , Zhang Haotian , Yang Xiaojun , Sun Qingzhu
Published: August 2021

Comprehensive microbial analysis has revealed that the lung harbors a complex variety of microbiota, and although the dynamic distribution of the lung microbiota in mice and laying hens of different ages is well established, this distribution has not been clarified in broilers of different ages. Here, we performed 16S rRNA gene sequencing of lung lavage fluid from broilers at 3 (3D), 7 (7D), 14 (14D), 21 (21D), and 35 (35D) days of age to evaluate changes in the composition of their lung microbiota. Upon examination of the composition and function of the broiler lung microbiota, we found that their maturation increased significantly with age. Specifically, the microbiota composition was similar between 7 and 14D and between 21 and 35D. The relative abundance of aerobic bacteria in the broiler lungs gradually increased as the broilers developed, whereas the relative abundance of potentially pathogenic bacteria reached its highest level at 3D. The relative abundance of predicted functions in microbiota was very similar among 3, 7, and 14D, whereas the Glycan Biosynthesis and Metabolism pathway in microbiota was enriched at 21D. These findings suggest that these metabolic pathways play critical roles in shaping broiler microbiota at these age stages. In addition, short-term external ammonia stimulation significantly increased lung inflammation but did not significantly affect the lung microbiota. Taken together, these data reveal the dynamics of age-related changes in the microbiota of broiler lungs and the stability (the significant variation in the microbial composition) of these microbial communities in response to short-term ammonia stress. These findings provide new insights into the development of broiler lung microbiota and serve as a reference for subsequent studies to evaluate disease prevention in broilers subjected to large-scale breeding.
Shedding Light on the Formation and Structure of Kombucha Biofilm Using Two-Photon Fluorescence Microscopy
Authors: Tran Thierry , Grandvalet Cosette , Winckler Pascale , Verdier François , Martin Antoine , Alexandre Hervé , Tourdot-Maréchal Raphaëlle
Published: August 2021

Kombucha pellicles are often used as inoculum to produce this beverage and have become a signature feature. This cellulosic biofilm produced by acetic acid bacteria (AAB) involves yeasts, which are also part of the kombucha consortia. The role of microbial interactions in thede novoformation and structure of kombucha pellicles was investigated during the 3 days following inoculation, using two-photon microscopy coupled with fluorescent staining. Aggregated yeast cells appear to serve as scaffolding to which bacterial cellulose accumulates. This initial foundation leads to a layered structure characterized by a top cellulose-rich layer and a biomass-rich sublayer. This sublayer is expected to be the microbiologically active site for cellulose production and spatial optimization of yeast–AAB metabolic interactions. The pellicles then grow in thickness while expanding their layered organization. A comparison with pellicles grown from pure AAB cultures shows differences in consistency and structure that highlight the impact of yeasts on the structure and properties of kombucha pellicles.
The Incremental Prognostic Value of Hepatocyte Growth Factor in First-Ever Acute Ischemic Stroke: An Early Link Between Growth Factor and Interleukins
Authors: Li Fangfang , Liu Ping , Huang Yuyou , Li Lingzhi , Zhang Sijia , Yang Zhenhong , Wang Rongliang , Tao Zhen , Han Ziping , Fan Junfen , Zheng Yangmin , Zhao Haiping , Luo Yumin
Published: August 2021

Hepatocyte growth factor (HGF) is a potential prognostic factor for acute ischemic stroke (AIS). In this study, we sought to validate its earlier predictive accuracy within 24 h for first-ever AIS. Moreover, as HGF interacts with interleukins, their associations may lead to novel immunomodulatory therapeutic strategies. Patients with first-ever AIS (n = 202) within 24 h were recruited. Plasma HGF and related interleukin concentrations were measured by multiplex immunoassays. The primary and secondary outcomes were major disability (modified Rankin scale score ≥3) at 3 months after AIS and death, respectively. Elastic net regression was applied to screen variables associated with stroke outcome; binary multivariable logistic analysis was then used to explore the relationship between HGF level and stroke outcome. After multivariate adjustment, upregulated HGF levels were associated with an increased risk of the primary outcome (odds ratio, 7.606; 95% confidence interval, 3.090–18.726; p < 0.001). Adding HGF to conventional risk factors significantly improved the predictive power for unfavorable outcomes (continuous net reclassification improvement 37.13%, p < 0.001; integrated discrimination improvement 8.71%, p < 0.001). The area under the receiver operating characteristic curve value of the traditional model was 0.8896 and reached 0.9210 when HGF was introduced into the model. An elevated HGF level may also be a risk factor for mortality within 3 months poststroke. The HGF level was also positively correlated with IL-10 and IL-16 levels, and HGF before interaction with all interleukins was markedly negatively correlated with the lymphocyte/neutrophil ratio. HGF within 24 h may have prognostic potential for AIS. Our findings reinforce the link between HGF and interleukins.
Risk Stratification Tool for Ischemic Stroke: A Risk Assessment Model Based on Traditional Risk Factors Combined With White Matter Lesions and Retinal Vascular Caliber
Authors: Zhao Lu , Jiang Bin , Li Hongyang , Yang Xiufen , Cheng Xiaoyue , Hong Hui , Wang Yanling
Published: August 2021

Objective: This study aims to establish a risk assessment model based on traditional risk factors combined with the Fazekas classification of white matter lesions and retinal vascular caliber for screening the patients at high risk of ischemic stroke.

Methods: This study included 296 patients (128 cases of ischemic stroke and 168 cases in the normal control group). The basic data of the patients were collected. Color fundus photography was performed after pupil dilation, and the retinal vascular caliber was measured using semiautomated vascular measurement software (IVAN Software, Sydney, Australia). The severity of white matter lesions (WML) on cranial nuclear magnetic fluid-attenuated inversion recovery images were assessed using the Fazekas scale. Moreover, logistic regression analysis was used to establish different risk assessment models for ischemic stroke. The effects of models were evaluated through the receiver operating characteristic (ROC) curve and the Delong test compared area under the curve.

Results: The sensitivity and specificity of models 1 (the traditional risk factor model), 2 (the retinal vascular caliber model), 3 (the WML model), and 4 (the combined the traditional risk factor, WML and central retinal artery equivalent (CRAE) model) were 71 and 55%, 48 and 71%, 49 and 67%, and 68 and 68.5% with areas under the curve of 0.658, 0.586, 0.601, and 0.708, respectively. The area under the receiver operating characteristic curve in models 1, 2, 3, and 4 showed statistically significant differences. Moreover, no statistical significance exists in the pairwise comparison of other models.

Conclusion: The risk assessment model of ischemic stroke combined with Fazekas grade of WML and CRAE is superior to the traditional risk factor and the single-index model. This model is helpful for risk stratification of high-risk stroke patients.
Evolving Trends in Surgical Management of Breast Cancer: An Analysis of 30 Years of Practice Changing Papers
Authors: Keelan Stephen , Flanagan Michael , Hill Arnold D. K.
Published: August 2021

The management of breast cancer has evolved into a multidisciplinary evidence-based surgical speciality, with emphasis on conservative surgery. A number of landmark trials have established lumpectomy followed by radiation as the standard of care for many patients. The aim of this study is to construct a narrative review of recent developments in the surgical management of breast cancer and how such developments have impacted surgical practice. A comprehensive literature search of Pubmed was conducted. The latest search was performed on October 31st, 2020. Search terms “breast cancer” were used in combinations with specific key words and Boolean operators relating to surgical management. The reference lists of retrieved articles were comprehensively screened for additional eligible publications. Articles were selected and reviewed based on relevance. We selected publications in the past 10 years but did not exclude commonly referenced and highly regarded previous publications. Review articles and book chapters were also cited to provide reference on details not discussed in the academic literature. This article reviews the current evidence in surgical management of early-stage breast cancer, discusses recent trends in surgical practice for therapeutic and prophylactic procedures and provides commentary on implications and factors associated with these trends.
Combining Clinicopathological Parameters and Molecular Indicators to Predict Lymph Node Metastasis in Endometrioid Type Endometrial Adenocarcinoma
Authors: Jiang Peng , Huang Yuzhen , Tu Yuan , Li Ning , Kong Wei , Di Feiyao , Jiang Shan , Zhang Jingni , Yi Qianlin , Yuan Rui
Published: August 2021

Background

Lymph node metastasis (LNM) is a critical unfavorable prognostic factor in endometrial cancer (EC). At present, models involving molecular indicators that accurately predict LNM are still uncommon. We addressed this gap by developing nomograms to individualize the risk of LNM in EC and to identify a low-risk group for LNM.

Methods

In all, 776 patients who underwent comprehensive surgical staging with pelvic lymphadenectomy at the First Affiliated Hospital of Chongqing Medical University were divided into a training cohort (used for building the model) and a validation cohort (used for validating the model) according to a predefined ratio of 7:3. Logistics regression analysis was used in the training cohort to screen out predictors related to LNM, after which a nomogram was developed to predict LNM in patients with EC. A calibration curve and consistency index (C-index) were used to estimate the performance of the model. A receiver operating characteristic (ROC) curve and Youden index were used to determine the optimal threshold of the risk probability of LNM predicted by the model proposed in this study. Then, the prediction performance of different models and their discrimination abilities for identifying low-risk patients were compared.

Result

LNM occurred in 87 and 42 patients in the training and validation cohorts, respectively. Multivariate logistic regression analysis showed that histological grade (P=0.022), myometrial invasion (P=0.002), lymphovascular space invasion (LVSI) (P=0.001), serum CA125 (P=0.008), Ki67 (P=0.012), estrogen receptor (ER) (0.009), and P53 (P=0.003) were associated with LNM; a nomogram was then successfully established on this basis. The internal and external calibration curves showed that the model fits well, and the C-index showed that the prediction accuracy of the model proposed in this study was better than that of the other models (the C-index of the training and validation cohorts was 0.90 and 0.91, respectively). The optimal threshold of the risk probability of LNM predicted by the model was 0.18. Based on this threshold, the model showed good discrimination for identifying low-risk patients.

Conclusion

Combining molecular indicators based on classical clinical parameters can predict LNM of patients with EC more accurately. The nomogram proposed in this study showed good discrimination for identifying low-risk patients with LNM.
Evaluation of the Diagnostic Potential of a Plasma Exosomal miRNAs Panel for Gastric Cancer
Authors: Yang Jiajia , Li Xuan , Wei Shuchun , Peng Lei , Sang Huaiming , Jin Duochen , Chen Meihong , Dang Yini , Zhang Guoxin
Published: August 2021

Purpose

Gastric cancer (GC) is often difficult to diagnose early in the disease and remains one of the most frequently occurring malignancies. This investigation looks at the diagnostic potential of a specific plasma exosomal miRNAs panel for GC.

Methods

This study analyzed 216 individual peripheral blood samples. 2 GEO datasets were analyzed and two miRNAs were selected - plasma exosomal miR-195-5p and miR-211-5p. Quantitative reverse-transcriptase PCR (qRT–PCR) was used to assess relative expressions and receiver operating characteristic (ROC) curve analysis was used to determine the diagnostic efficiency of miR-195-5p and miR-211-5p panel. The Kaplan-Meier method was used to assess the prognostic value of plasma exosomal miR-195-5p and miR-211-5p.

Results

GC patients possessed notably raised plasma levels of exosomal miR-195-5p and miR-211-5p. The area under ROC curves (AUCs) of miR-195-5p, miR-211-5p were 0.745, 0.798 in the screening phase and 0.762, 0.798 in the training stage respectively. GC was able to be diagnosed more accurately when both miRNAs were interpreted together (AUC=0.820 in the validation stage). Poorer prognosis was observed in GC patients who had plasma exosomal miR-195-5p and miR-211-5p of higher levels. In vitro experiments also confirmed that miR-195-5p and miR-211-5p is able to be transmitted between cells, and works to enhance tumor invasion, migration and proliferation while inhibiting cell apoptosis.

Conclusion

Plasma exosomal miR-195-5p and miR-211-5p may become potential biomarkers for GC diagnosis, and may be useful in predicting tumor phenotype.
Microglia-Specific Expression of HEXA and HEXB Leads to Poor Prognosis in Glioblastoma Patients
Authors: Jia Mengxian , Zhang Wenbin , Zhu Junle , Huang Changgang , Zhou Jian , Lian Jiashu , Wang Ying , Teng Honglin , Huang Zhihui
Published: August 2021

Glioblastoma multiforme (GBM) is one of the deadliest cancers in brain. There have been few treatment advances for GBM despite increasing scientific understanding of this disease. β-hexosaminidase (Hex) is an important enzyme system in human body, encoded by two genes, HEXA and HEXB, are closely related to central nervous system (CNS) diseases such as Sandhoff disease (SD) and Tay-Sachs disease (TSD). However, the expression pattern and function of HEXA and HEXB in GBM remains unclear. Here, we found that both the mRNA and protein expression levels of HEXA and HEXB were significantly upregulated in GBM patient samples. The results from single-cell RNA-sequencing (scRNA-seq) database and double immunostaining showed that HEXA and HEXB were specifically expressed in microglia in GBM patient samples. Furthermore, our in vitro experiments revealed that conditioned media from HEXA and HEXB knockdown-microglia cells could inhibit the proliferation and migration of GBM cells. Finally, according to survival analysis based on online database, higher expression of HEXA and HEXB was associated with poor prognosis in GBM patients. In conclusion, these results suggest that microglial HEXA and HEXB play fundamental role in GBM progression, and they will be potential biomarkers for GBM.
Comprehensive Analysis of a tRNA-Derived Small RNA in Colorectal Cancer
Authors: Zhu Yong , Chen Shaoqiu , Ling Zhougui , Winnicki Andrew , Xu Lilly , Xu Shaun , Gong Ting , Jiang Bin , Huang Gang , Deng Youping
Published: August 2021

Colorectal cancer often presents as a highly variable disease with myriad forms that are at times difficult to detect in early screenings with sufficient accuracy, for which novel diagnostic methods are an attractive and valuable area of improvement. To improve colorectal cancer diagnosis and prognosis, new biomarkers that can be assembled into a diagnostic panel must be identified, and tRNA-derived small RNAs (tsRNAs) are a particularly interesting and increasingly visible new class of molecules to examine. In this study, small RNA-seq data were profiled for the expression of 104 human tsRNAs in tumor tissue and adjacent normal tissue samples, and a diagnostic model was built based on four differentially expressed tsRNAs: tRF-22-WB86Q3P92, tRF-22-WE8SPOX52, tRF-22-WE8S68L52, tRF-18-8R1546D2. Furthermore, the diagnostic model was validated by two independent validation datasets (AUC was 0.97 and 0.99), and a LASSO model was applied to develop a seven-tsRNA-based risk score model for colorectal cancer prognosis. Finally, a tsRNA-mRNA interaction network was established according to potential mRNA targets predicted by bioinformatic methods. In conclusion, the results suggest that abnormal expression of tsRNA in colorectal cancer may have a functional effect on tumor action and moreover, that some of the tsRNAs identified in this study with diagnostic and prognostic potential could be of clinical significance.
Decoupling Lineage-Associated Genes in Acute Myeloid Leukemia Reveals Inflammatory and Metabolic Signatures Associated With Outcomes
Authors: Abbas Hussein A. , Mohanty Vakul , Wang Ruiping , Huang Yuefan , Liang Shaoheng , Wang Feng , Zhang Jianhua , Qiu Yihua , Hu Chenyue W. , Qutub Amina A. , Dail Monique , Bolen Christopher R. , Daver Naval , Konopleva Marina , Futreal Andrew , Chen Ken , Wang Linghua , Kornblau Steven M.
Published: August 2021

Acute myeloid leukemia (AML) is a heterogeneous disease with variable responses to therapy. Cytogenetic and genomic features are used to classify AML patients into prognostic and treatment groups. However, these molecular characteristics harbor significant patient-to-patient variability and do not fully account for AML heterogeneity. RNA-based classifications have also been applied in AML as an alternative approach, but transcriptomic grouping is strongly associated with AML morphologic lineages. We used a training cohort of newly diagnosed AML patients and conducted unsupervised RNA-based classification after excluding lineage-associated genes. We identified three AML patient groups that have distinct biological pathways associated with outcomes. Enrichment of inflammatory pathways and downregulation of HOX pathways were associated with improved outcomes, and this was validated in 2 independent cohorts. We also identified a group of AML patients who harbored high metabolic and mTOR pathway activity, and this was associated with worse clinical outcomes. Using a comprehensive reverse phase protein array, we identified higher mTOR protein expression in the highly metabolic group. We also identified a positive correlation between degree of resistance to venetoclax and mTOR activation in myeloid and lymphoid cell lines. Our approach of integrating RNA, protein, and genomic data uncovered lineage-independent AML patient groups that share biologic mechanisms and can inform outcomes independent of commonly used clinical and demographic variables; these groups could be used to guide therapeutic strategies.
Clinicopathologic and Molecular Characteristics of Gastrointestinal MiNENs
Authors: Yeo Min-Kyung , Yoon Nara , Bae Go Eun
Published: August 2021

Background

A mixed neuroendocrine–non-neuroendocrine neoplasm (MiNEN) is a recently defined entity that comprises a neuroendocrine tumor (NEN) component and a non-neuroendocrine tumor (nNEN) component. As MiNEN is a recently defined entity, its molecular nature is not well known. Here, we evaluated the clinicopathologic and molecular characteristics of gastrointestinal (GI) MiNENs.

Methods

We performed a genomic analysis of 31 samples from 12 GI MiNEN cases using next-generation sequencing. We examined the primary NEN and nNEN components, as well as the metastatic NENs and nNENs. The relationships between the clinical tumor features (component, location, and grade) and their molecular characteristics were examined.

Results

The 12 MiNENs included in the study were found in the stomach (n=10), distal rectum (n=1), and anus (n=1). Primary MiNENs that had NENs as the major component showed a worse clinical outcome than those that had nNENs as the major component. All distant metastatic tumors originating from MiNENs were NENs. In addition, NENs generally carried 1.5 times more gene mutations and copy number variations than nNENs. The ATRX gene deletion and TP53 gene mutation were the most common variants in both components of GI MiNENs.

Conclusions

We have revealed the detailed clinicopathologic and molecular findings with distinguishable alterations of GI MiNENs. To our knowledge, this is the first study to report the ATRX gene deletion in GI MiNENs. The molecular characteristics of GI MiNENs could provide clues to the pathogenic origin and progression of GI MiNENs.
IL6 and BCL3 Expression Are Potential Biomarkers in Esophageal Squamous Cell Carcinoma
Authors: Soares-Lima Sheila Coelho , Gonzaga Isabela Martins , Camuzi Diego , Nicolau-Neto Pedro , Vieira da Silva Raissa , Guaraldi Simone , Ferreira Maria Aparecida , Hernandez-Vargas Hector , Herceg Zdenko , Ribeiro Pinto Luis Felipe
Published: August 2021

Esophageal squamous cell carcinoma (ESCC) ranks among the most lethal tumors worldwide, as a consequence of late detection and poor treatment response, evidencing the need for diagnosis anticipation and new therapeutic targets. First, we investigated the IL6 gene and protein expression in the esophagus of individuals without esophageal disorders (healthy), ESCC, and non-tumoral surrounding tissue (NTST). Our results showed that IL6 mRNA and protein expression is upregulated in tumor cells relative to NTST. In the TCGA dataset, we identified a set of genes whose expression was correlated with IL6 mRNA levels, including the antiapoptotic gene BCL3. By using an immortalized esophageal cell line, we confirmed that IL6 was capable of inducing BCL3 expression in esophageal cells. BCL3 mRNA and protein are overexpressed in ESCC and NTST compared to healthy esophagus, and BCL3 mRNA could distinguish the morphologically normal samples (healthy and NTST) with 100% sensitivity and 95.12% specificity. The spatial intratumoral heterogeneity of both IL6 and BCL3 expression was evaluated, corroborating IL6 upregulation throughout the tumor, while tumor and NTST showed a consistent increase of BCL3 expression relative to the healthy esophagus. Our study shows that IL6 overexpression seems to be a key event in ESCC carcinogenesis, contributing to ESCC through a homogeneous antiapoptotic signalling via BCL3 overexpression, thus suggesting anti-IL6 therapies to be further considered for ESCC treatment. Finally, our data support the use of BCL3 mRNA expression as a potential biomarker for ESCC detection.
Therapeutic Sequences in the Treatment of High-Risk Prostate Cancer: Paving the Way Towards Multimodal Tailored Approaches
Authors: Marvaso Giulia , Corrao Giulia , Zaffaroni Mattia , Pepa Matteo , Augugliaro Matteo , Volpe Stefania , Musi Gennaro , Luzzago Stefano , Mistretta Francesco Alessandro , Verri Elena , Cossu Rocca Maria , Ferro Matteo , Petralia Giuseppe , Nolè Franco , De Cobelli Ottavio , Orecchia Roberto , Jereczek-Fossa Barbara Alicja
Published: August 2021

Various definitions are currently in use to describe high-risk prostate cancer. This variety in definitions is important for patient counseling, since predicted outcomes depend on which classification is applied to identify patient’s prostate cancer risk category. Historically, strategies for the treatment of localized high-risk prostate cancer comprise local approaches such as surgery and radiotherapy, as well as systemic approaches such as hormonal therapy. Nevertheless, since high-risk prostate cancer patients remain the group with higher-risk of treatment failure and mortality rates, nowadays, novel treatment strategies, comprising hypofractionated-radiotherapy, second-generation antiandrogens, and hadrontherapy, are being explored in order to improve their long-term oncological outcomes. This narrative review aims to report the current management of high-risk prostate cancer and to explore the future perspectives in this clinical setting.
Congenital Bronchobiliary Fistula: A Case Report and Literature Review
Authors: Bing Zhen , Chen Rui , Xing Pengchao , Ren Yueyi , Hou Kefeng
Published: August 2021

Congenital bronchobiliary fistula (CBBF) is a rare disease. Children with CBBF mostly have atypical clinical manifestations that can be easily missed. We report a case of a child with CBBF who was diagnosed with fistulography with the help of an endobronchial blocker and a fiberoptic bronchoscope. The CBBF was successfully removed by thoracoscopic surgery.