bluuebunny/crossref_metadata_2025 huggingface dataset:
GeenaR: A Web Tool for Reproducible MALDI-TOF Analysis
Authors: Del Prete Eugenio , Facchiano Angelo , Profumo Aldo , Angelini Claudia , Romano Paolo
Published: March 2021

Mass spectrometry is a widely applied technology with a strong impact in the proteomics field. MALDI-TOF is a combined technology in mass spectrometry with many applications in characterizing biological samples from different sources, such as the identification of cancer biomarkers, the detection of food frauds, the identification of doping substances in athletes’ fluids, and so on. The massive quantity of data, in the form of mass spectra, are often biased and altered by different sources of noise. Therefore, extracting the most relevant features that characterize the samples is often challenging and requires combining several computational methods. Here, we present GeenaR, a novel web tool that provides a complete workflow for pre-processing, analyzing, visualizing, and comparing MALDI-TOF mass spectra. GeenaR is user-friendly, provides many different functionalities for the analysis of the mass spectra, and supports reproducible research since it produces a human-readable report that contains function parameters, results, and the code used for processing the mass spectra. First, we illustrate the features available in GeenaR. Then, we describe its internal structure. Finally, we prove its capabilities in analyzing oncological datasets by presenting two case studies related to ovarian cancer and colorectal cancer. GeenaR is available at http://proteomics.hsanmartino.it/geenar/.
Full-Length Transcriptome Analyses of Genes Involved in Triterpenoid Saponin Biosynthesis of Psammosilene tunicoides Hairy Root Cultures With Exogenous Salicylic Acid
Authors: Su Lingye , Li Shufang , Qiu Hanhan , Wang Hongfeng , Wang Congcong , He Chunmei , Xu Mingfeng , Zhang Zongshen
Published: March 2021

Triterpenoid saponins constitute a diverse class of bioactive compounds in medicinal plants. Salicylic acid (SA) is an efficient elicitor for secondary metabolite production, but a transcriptome-wide regulatory network of SA-promoted triterpenoid saponin biosynthesis remains little understood. In the current study, we described the establishment of the hairy root culture system for Psammosilene tunicoides, a triterpenoid saponin-producing medicinal herb in China, using genetic transformation by Agrobacterium rhizogenes. Compared to controls, we found that total saponin content was dramatically increased (up to 2.49-fold) by the addition of 5 mg/L SA in hairy roots for 1 day. A combination of single-molecule real-time (SMRT) and next-generation sequencing (Illumina RNA-seq) was generated to analyze the full-length transcriptome data for P. tunicoides, as well as the transcript profiles in treated (8 and 24 h) and non-treated (0 h) groups with 5 mg/L SA in hairy roots. A total of 430,117 circular consensus sequence (CCS) reads, 16,375 unigenes and 4,678 long non-coding RNAs (lncRNAs) were obtained. The average length of unigenes (2,776 bp) was much higher in full-length transcriptome than that derived from single RNA-seq (1,457 bp). The differentially expressed genes (DEGs) were mainly enriched in the metabolic process. SA up-regulated the unigenes encoding SA-binding proteins and antioxidant enzymes in comparison with controls. Additionally, we identified 89 full-length transcripts encoding enzymes putatively involved in saponin biosynthesis. The candidate transcription factors (WRKY, NAC) and structural genes (AACT, DXS, SE, CYP72A) might be the key regulators in SA-elicited saponin accumulation. Their expression was further validated by quantitative real-time PCR (qRT-PCR). These findings preliminarily elucidate the regulatory mechanisms of SA on triterpenoid saponin biosynthesis in the transcriptomic level, laying a foundation for SA-elicited saponin augmentation in P. tunicoides.
Deciphering Myostatin’s Regulatory, Metabolic, and Developmental Influence in Skeletal Diseases
Authors: Omosule Catherine L. , Phillips Charlotte L.
Published: March 2021

Current research findings in humans and other mammalian and non-mammalian species support the potent regulatory role of myostatin in the morphology and function of muscle as well as cellular differentiation and metabolism, with real-life implications in agricultural meat production and human disease. Myostatin null mice (mstn−/−) exhibit skeletal muscle fiber hyperplasia and hypertrophy whereas myostatin deficiency in larger mammals like sheep and pigs engender muscle fiber hyperplasia. Myostatin’s impact extends beyond muscles, with alterations in myostatin present in the pathophysiology of myocardial infarctions, inflammation, insulin resistance, diabetes, aging, cancer cachexia, and musculoskeletal disease. In this review, we explore myostatin’s role in skeletal integrity and bone cell biology either due to direct biochemical signaling or indirect mechanisms of mechanotransduction. In vitro, myostatin inhibits osteoblast differentiation and stimulates osteoclast activity in a dose-dependent manner. Mice deficient in myostatin also have decreased osteoclast numbers, increased cortical thickness, cortical tissue mineral density in the tibia, and increased vertebral bone mineral density. Further, we explore the implications of these biochemical and biomechanical influences of myostatin signaling in the pathophysiology of human disorders that involve musculoskeletal degeneration. The pharmacological inhibition of myostatin directly or via decoy receptors has revealed improvements in muscle and bone properties in mouse models of osteogenesis imperfecta, osteoporosis, osteoarthritis, Duchenne muscular dystrophy, and diabetes. However, recent disappointing clinical trial outcomes of induced myostatin inhibition in diseases with significant neuromuscular wasting and atrophy reiterate complexity and further need for exploration of the translational application of myostatin inhibition in humans.
uhrf1 and dnmt1 Loss Induces an Immune Response in Zebrafish Livers Due to Viral Mimicry by Transposable Elements
Authors: Magnani Elena , Macchi Filippo , Madakashira Bhavani P. , Zhang Chi , Alaydaroos Fatima , Sadler Kirsten C.
Published: March 2021

Activation of transposable elements (TEs) can cause cellular damage. Cytoplasmic nucleic acid sensing pathways evolved to detect pathogens, but can also serve to cull cells with inappropriate TE activation as TEs can be viral mimetics. Epigenetic silencing of TEs is mediated in part by DNA methylation, but it is not clear if TE activation or the immune system contribute to the cellular damage caused by loss of DNA methylation. Here, we provide mechanistic insight into the observation of an activated interferon response in the liver of zebrafish larvae with deletion in critical components of the DNA methylation machinery, uhrf1 and dnmt1. We focus on dissecting the relationship between DNA methylation, TE activation and induction of an immune response through cytoplasmic DNA and double stranded RNA sensing pathways and identify tnfa as a mediator of cell death in the liver of these mutants. Integrated RNAseq and methylome analysis identified LTR transposons as the most upregulated in these mutants and also the most methylated in control larvae, indicating a direct role of DNA methylation in suppressing this TE subclass. RNAseq analysis from these same samples revealed expression signatures of a type-I interferon response and of tnfa activation, mimicking the pattern of gene expression in virally infected cells. CRISPR/Cas9 mediated depletion of the cellular antiviral sensors sting and mavs reduced expression of interferon response genes and tnfa depletion dramatically reduced cell death in uhrf1 mutant livers. This suggests that the antiviral response induced by DNA hypomethylation and TE activation in the liver is mediated by the signaling pathways activated by both cytoplasmic double stranded RNA and DNA and that tnfa mediates cell death as a potential mechanism to eliminate these damaged cells.
Magnitude of Off-Target Allo-HLA Reactivity by Third-Party Donor-Derived Virus-Specific T Cells Is Dictated by HLA-Restriction
Authors: Huisman Wesley , Leboux Didier A. T. , van der Maarel Lieve E. , Hageman Lois , Amsen Derk , Falkenburg J. H. Frederik , Jedema Inge
Published: March 2021

T-cell products derived from third-party donors are clinically applied, but harbor the risk of off-target toxicity via induction of allo-HLA cross-reactivity directed against mismatched alleles. We used third-party donor-derived virus-specific T cells as model to investigate whether virus-specificity, HLA restriction and/or HLA background can predict the risk of allo-HLA cross-reactivity. Virus-specific CD8pos T cells were isolated from HLA-A*01:01/B*08:01 or HLA-A*02:01/B*07:02 positive donors. Allo-HLA cross-reactivity was tested using an EBV-LCL panel covering 116 allogeneic HLA molecules and confirmed using K562 cells retrovirally transduced with single HLA-class-I alleles of interest. HLA-B*08:01-restricted T cells showed the highest frequency and diversity of allo-HLA cross-reactivity, regardless of virus-specificity, which was skewed toward multiple recurrent allogeneic HLA-B molecules. Thymic selection for other HLA-B alleles significantly influenced the level of allo-HLA cross-reactivity mediated by HLA-B*08:01-restricted T cells. These results suggest that the degree and specificity of allo-HLA cross-reactivity by T cells follow rules. The risk of off-target toxicity after infusion of incompletely matched third-party donor-derived virus-specific T cells may be reduced by selection of T cells with a specific HLA restriction and background.
Single-Cell Transcriptomics and In Situ Morphological Analyses Reveal Microglia Heterogeneity Across the Nigrostriatal Pathway
Authors: Uriarte Huarte Oihane , Kyriakis Dimitrios , Heurtaux Tony , Pires-Afonso Yolanda , Grzyb Kamil , Halder Rashi , Buttini Manuel , Skupin Alexander , Mittelbronn Michel , Michelucci Alessandro
Published: March 2021

Microglia are the resident immune effector cells of the central nervous system (CNS) rapidly reacting to various pathological stimuli to maintain CNS homeostasis. However, microglial reactions in the CNS may also worsen neurological disorders. Hence, the phenotypic analysis of microglia in healthy tissue may identify specific poised subsets ultimately supporting or harming the neuronal network. This is all the more important for the understanding of CNS disorders exhibiting regional-specific and cellular pathological hallmarks, such as many neurodegenerative disorders, including Parkinson’s disease (PD). In this context, we aimed to address the heterogeneity of microglial cells in susceptible brain regions for PD, such as the nigrostriatal pathway. Here, we combined single-cell RNA-sequencing with immunofluorescence analyses of the murine nigrostriatal pathway, the most affected brain region in PD. We uncovered a microglia subset, mainly present in the midbrain, displaying an intrinsic transcriptional immune alerted signature sharing features of inflammation-induced microglia. Further, an in situ morphological screening of inferred cellular diversity showed a decreased microglia complexity in the midbrain when compared to striatum. Our study provides a resource for the identification of specific microglia phenotypes within the nigrostriatal pathway, which may be relevant in PD.
A New Method for Investigating Relationships Between Distribution of Sessile Organisms and Multiple Terrain Variables by Photogrammetry of Subtidal Bedrocks
Authors: Kanki Takayuki , Nakamoto Kenta , Hayakawa Jun , Kitagawa Takashi , Kawamura Tomohiko
Published: March 2021

Previous studies of habitat suitability of sessile organisms on subtidal rocky substrata have been focused only one or two terrain attributes. In this study, we propose a new method to construct a centimeter resolution seafloor topographic model by using underwater photogrammetry to obtain multiple terrain variables and to investigate relationships between the distribution of sessile organisms and multiple terrain variables. Point cloud models of five square sections (11.3–25.5 m2) of the bedrock surface of Otsuchi Bay were reconstructed with a 0.05 m resolution. Using the 0.01 m resolution point cloud models, five terrain variables were calculated on each face of the mesh models: height above seafloor, topological position index, slope, aspect, and ruggedness. The presence/absence data of four species of sessile organisms (ascidian Halocynthia roretzi, barnacle Balanus trigonus, polychaete Paradexiospira nakamurai, and articulated coralline algae Pachyarthron cretaceum) were located on the mesh models. H. roretzi and B. trigonus were more abundant on vertical and high faces above the seafloor, and P. nakamurai were more abundant at high faces above the surroundings. In high position where the current velocity increases, the three sessile animals may have an advantage for their suspension feeding. In contrast, P. cretaceum, unlike the other three sessile animal species, occurred at various heights and on gentle slope faces suitable for photosynthesis.
Conservation Opportunities Arise From the Co-Occurrence of Surfing and Key Biodiversity Areas
Authors: Reineman Dan R. , Koenig Kellee , Strong-Cvetich Nik , Kittinger John N.
Published: March 2021

Conserving biodiversity and ecosystem services requires diverse models that empower communities to steward and benefit from resources. Here we investigate the potential of surfing resources, a new conservation asset class, and the surfing community, an underutilized conservation constituency, to conserve marine biodiversity. We conducted a spatial analysis of the overlap among Key Biodiversity Areas, Marine Protected Areas (MPAs), and 3,755 surf breaks globally. We find that 62.77% of surf breaks are not within MPAs and that 25.81% of all surf breaks are within 5 km of a Key Biodiversity Area, but are not within a MPA, suggesting that strategic conservation opportunities arise from the co-occurrence of surfing resources and biodiversity priorities. Establishing or extending protections to surfing ecosystems could increase protection for biodiversity at one-quarter of surf breaks. Sustainable management of these resources ensures their ability to provide for the character, economy, and development of coastal communities worldwide.
COVID-19 Pandemic: Advances in Diagnosis, Treatment, Organoid Applications and Impacts on Cancer Patient Management
Authors: Ye Chenyang , Qi Lina , Wang Ji , Zheng Shu
Published: March 2021

Coronavirus disease 2019 (COVID-19) caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread globally and rapidly developed into a worldwide pandemic. The sudden outburst and rapid dissemination of SARS-CoV-2, with overwhelming public health and economic burdens, highlight an urgent need to develop effective strategies for the diagnosis and treatment of infected patients. In this review, we focus on the current advances in the diagnostics and treatment for SARS-CoV-2 infection. Notably, we also summarize some antineoplastic drugs repurposed for COVID-19 treatment and address the diagnostic and therapeutic challenges for oncologists to manage cancer patients in this COVID-19 era. In addition, we emphasize the importance of organoid technology as a valuable experimental virology platform to better understand the pathogenesis of COVID-19 and assist rapid screening of drugs against COVID-19.
Hepatic Steatosis, Rather Than Underlying Obesity, Increases the Risk of Infection and Hospitalization for COVID-19
Authors: Roca-Fernández Adriana , Dennis Andrea , Nicholls Rowan , McGonigle John , Kelly Matthew , Banerjee Rajarshi , Banerjee Amitava , Sanyal Arun J.
Published: March 2021

Objective: Obesity is a risk factor for SARS-COV2 infection and is often associated with hepatic steatosis. The aim of this study was to determine if pre-existing hepatic steatosis affects the risk of infection and severity for COVID-19.

Design: Prospective cohort study (UK Biobank). Univariate and stepwise multivariate logistic regression analyses were performed on liver phenotypic biomarkers to determine if these variables increased risk of testing positive and being hospitalized for COVID-19; then compared to previously described risk factors associated with COVID-19, including age, ethnicity, gender, obesity, socio-economic status.

Setting: UK biobank study.

Participants: 502,506 participants (healthy at baseline) in the UK Biobank, of whom 41,791 underwent MRI (aged 50–83) for assessment of liver fat, liver fibro-inflammatory disease, and liver iron. Positive COVID-19 test was determined from UK testing data, starting in March 2020 and censored in January 2021.

Primary and Secondary Outcome Measures: Liver fat measured as proton density fat fraction (PDFF%) MRI and body mass index (BMI, Kg/m2) to assess prior to February 2020 using MRI of the liver to assess hepatic steatosis.

Results: Within the imaged cohort (n = 41, 791), 4,458 had been tested and 1,043 (2.49% of the imaged population) tested positive for COVID-19. Individuals with fatty liver (≥10%) were at increased risk of testing positive (OR: 1.35, p = 0.007) and those participants with obesity and fatty liver, were at increased risk of hospitalization with a positive test result by 5.14 times (p = 0.0006).

Conclusions: UK Biobank data revealed obese individuals with fatty liver disease were at increased risk of infection and hospitalization for COVID-19. Public policy measures and personalized medicine should be considered in order to protect these high-risk individuals.
The Quest for System-Theoretical Medicine in the COVID-19 Era
Authors: Tretter Felix , Wolkenhauer Olaf , Meyer-Hermann Michael , Dietrich Johannes W. , Green Sara , Marcum James , Weckwerth Wolfram
Published: March 2021

Precision medicine and molecular systems medicine (MSM) are highly utilized and successful approaches to improve understanding, diagnosis, and treatment of many diseases from bench-to-bedside. Especially in the COVID-19 pandemic, molecular techniques and biotechnological innovation have proven to be of utmost importance for rapid developments in disease diagnostics and treatment, including DNA and RNA sequencing technology, treatment with drugs and natural products and vaccine development. The COVID-19 crisis, however, has also demonstrated the need for systemic thinking and transdisciplinarity and the limits of MSM: the neglect of the bio-psycho-social systemic nature of humans and their context as the object of individual therapeutic and population-oriented interventions. COVID-19 illustrates how a medical problem requires a transdisciplinary approach in epidemiology, pathology, internal medicine, public health, environmental medicine, and socio-economic modeling. Regarding the need for conceptual integration of these different kinds of knowledge we suggest the application of general system theory (GST). This approach endorses an organism-centered view on health and disease, which according to Ludwig von Bertalanffy who was the founder of GST, we call Organismal Systems Medicine (OSM). We argue that systems science offers wider applications in the field of pathology and can contribute to an integrative systems medicine by (i) integration of evidence across functional and structural differentially scaled subsystems, (ii) conceptualization of complex multilevel systems, and (iii) suggesting mechanisms and non-linear relationships underlying the observed phenomena. We underline these points with a proposal on multi-level systems pathology including neurophysiology, endocrinology, immune system, genetics, and general metabolism. An integration of these areas is necessary to understand excess mortality rates and polypharmacological treatments. In the pandemic era this multi-level systems pathology is most important to assess potential vaccines, their effectiveness, short-, and long-time adverse effects. We further argue that these conceptual frameworks are not only valid in the COVID-19 era but also important to be integrated in a medicinal curriculum.
Antibiotics and Antibiotic Resistance Genes in Animal Manure – Consequences of Its Application in Agriculture
Authors: Zalewska Magdalena , Błażejewska Aleksandra , Czapko Agnieszka , Popowska Magdalena
Published: March 2021

Antibiotic resistance genes (ARGs) are a relatively new type of pollutant. The rise in antibiotic resistance observed recently is closely correlated with the uncontrolled and widespread use of antibiotics in agriculture and the treatment of humans and animals. Resistant bacteria have been identified in soil, animal feces, animal housing (e.g., pens, barns, or pastures), the areas around farms, manure storage facilities, and the guts of farm animals. The selection pressure caused by the irrational use of antibiotics in animal production sectors not only promotes the survival of existing antibiotic-resistant bacteria but also the development of new resistant forms. One of the most critical hot-spots related to the development and dissemination of ARGs is livestock and poultry production. Manure is widely used as a fertilizer thanks to its rich nutrient and organic matter content. However, research indicates that its application may pose a severe threat to human and animal health by facilitating the dissemination of ARGs to arable soil and edible crops. This review examines the pathogens, potentially pathogenic microorganisms and ARGs which may be found in animal manure, and evaluates their effect on human health through their exposure to soil and plant resistomes. It takes a broader view than previous studies of this topic, discussing recent data on antibiotic use in farm animals and the effect of these practices on the composition of animal manure; it also examines how fertilization with animal manure may alter soil and crop microbiomes, and proposes the drivers of such changes and their consequences for human health.
The CRISPR-Cas System Is Involved in OmpR Genetic Regulation for Outer Membrane Protein Synthesis in Salmonella Typhi
Authors: Medina-Aparicio Liliana , Rodriguez-Gutierrez Sarahí , Rebollar-Flores Javier E. , Martínez-Batallar Ángel G. , Mendoza-Mejía Blanca D. , Aguirre-Partida Eira D. , Vázquez Alejandra , Encarnación Sergio , Calva Edmundo , Hernández-Lucas Ismael
Published: March 2021

The CRISPR-Cas cluster is found in many prokaryotic genomes including those of the Enterobacteriaceae family. Salmonella enterica serovar Typhi (S. Typhi) harbors a Type I-E CRISPR-Cas locus composed of cas3, cse1, cse2, cas7, cas5, cas6e, cas1, cas2, and a CRISPR1 array. In this work, it was determined that, in the absence of cas5 or cas2, the amount of the OmpC porin decreased substantially, whereas in individual cse2, cas6e, cas1, or cas3 null mutants, the OmpF porin was not observed in an electrophoretic profile of outer membrane proteins. Furthermore, the LysR-type transcriptional regulator LeuO was unable to positively regulate the expression of the quiescent OmpS2 porin, in individual S. Typhi cse2, cas5, cas6e, cas1, cas2, and cas3 mutants. Remarkably, the expression of the master porin regulator OmpR was dependent on the Cse2, Cas5, Cas6e, Cas1, Cas2, and Cas3 proteins. Therefore, the data suggest that the CRISPR-Cas system acts hierarchically on OmpR to control the synthesis of outer membrane proteins in S. Typhi.
Up-Regulating ERIC by CRISPR-dCas9-VPR Inhibits Cell Proliferation and Invasion and Promotes Apoptosis in Human Bladder Cancer
Authors: Yang Jiangeng , Xia An , Zhang Huajie , Liu Qi , You Hongke , Ding Daoyuan , Yin Yonghua , Wen Bo
Published: March 2021

LncRNAs are defined as non-coding RNAs that are longer than 200 nucleotides in length. The previous studys has shown that lncRNAs played important roles in the regulation of gene expression and were essential in mammalian development and disease processes. Inspired by the observation that lncRNAs are aberrantly expressed in tumors, we extracted RNA from Bladder urothelial carcinoma and matched histologically normal urothelium from each patient and bladder carcinoma cell lines. Then, we reversed transcribed them into cDNA.Last, we investigated the expression patterns of ERIC by the fluorescence quantitative PCR in bladder cancer tissues and cell lines. CRISPR-dCas9-VPR targeting ERIC plasmid was transfected into T24 and 5637 cells, and cells were classified into two groups: negative control (NC) and ERIC overexpression group. MTT assay, transwell assay, and flow cytometry were performed to examine changes in cell proliferation, invasiveness, and apoptosis. We found that the expression of ERIC was down-regulated in bladder urothelial carcinoma compared to matched histologically normal urotheliam. The differences of the expression of this gene were large in the bladder cancer lines. Compared with the negative control group, the ERIC overexpression group showed significantly decreased cell proliferation rate (t = 7.583, p = 0.002; t = 3.283, p = 0.03) and invasiveness (t = 11.538, p < 0.001; t = 8.205, p = 0.01); and increased apoptotic rate (t = −34.083, p < 0.001; t = −14.316, p < 0.001). Our study lays a foundation for further study of its pathogenic mechanism in bladder cancer.
Destination Amyotrophic Lateral Sclerosis
Authors: Keon Matt , Musrie Benjamin , Dinger Marcel , Brennan Samuel E. , Santos Jerran , Saksena Nitin K.
Published: March 2021

Amyotrophic Lateral Sclerosis (ALS) is a prototypical neurodegenerative disease characterized by progressive degeneration of motor neurons both in the brain and spinal cord. The constantly evolving nature of ALS represents a fundamental dimension of individual differences that underlie this disorder, yet it involves multiple levels of functional entities that alternate in different directions and finally converge functionally to define ALS disease progression. ALS may start from a single entity and gradually becomes multifactorial. However, the functional convergence of these diverse entities in eventually defining ALS progression is poorly understood. Various hypotheses have been proposed without any consensus between the for-and-against schools of thought. The present review aims to capture explanatory hierarchy both in terms of hypotheses and mechanisms to provide better insights on how they functionally connect. We can then integrate them within a common functional frame of reference for a better understanding of ALS and defining future treatments and possible therapeutic strategies. Here, we provide a philosophical understanding of how early leads are crucial to understanding the endpoints in ALS, because invariably, all early symptomatic leads are underpinned by neurodegeneration at the cellular, molecular and genomic levels. Consolidation of these ideas could be applied to other neurodegenerative diseases (NDs) and guide further critical thinking to unveil their roadmap of destination ALS.
Prolonged Duration of Blood Pressure Drops During General Anesthesia Is Associated With Worse Outcomes After Mechanical Thrombectomy
Authors: Xu Chao , Lin Gaoping , Zhang Zheyu , Jin Tianyu , Li Ning , Mao Hui , Ye Sasa , Yang Zongming , Geng Yu , Shi Zongjie
Published: March 2021

Background and Purpose: Optimal periprocedural management of blood pressure during mechanical thrombectomy (MT) remains controversial. This study aimed to investigate the relationship between the duration of blood pressure drops during general anesthesia and the outcomes in large vessel occlusion (LVO) patients treated with MT.

Methods: We retrospectively reviewed our prospectively collected data for LVO patients treated with MT between January 2018 and July 2020. Intraprocedural mean arterial pressure (MAP) was recorded every 5 min throughout the procedure. Baseline MAP minus each MAP value recorded during general anesthesia was defined ΔMAP. Cumulated time (in min) and longest continuous episode (in min) with ΔMAP more than 10, 15, 20, 25, and 30 mmHg were calculated, respectively. Poor outcome was defined as 90-day modified Rankin score (mRS) 3–6. Associations between cumulated time of different ΔMAP thresholds and poor outcome were determined using binary logistic regression models.

Results: A total of 131 patients were finally included in the study. After controlling for age, atrial fibrillation, baseline NIHSS, baseline ASPECTS, procedure duration of MT, and times of retrieval attempts, the results indicated that cumulated time of MAP drop more than 10 mmHg (OR 1.013; 95% CI 1.004–1.023; P = 0.007) and 15 mmHg (OR 1.011; 95% CI 1.002–1.020; P = 0.017) were independently associated with poor outcomes.

Conclusion: Prolonged episodes of intraprocedural MAP lowering were more likely to have poor outcomes in LVO patients following MT with general anesthesia, which might be helpful in guiding intraprocedural hemodynamic management of patients under general anesthesia.
Comparison of Pattern Discrimination Mechanisms of Hebbian and Spatiotemporal Learning Rules in Self-Organization
Authors: Tsukada Hiromichi , Tsukada Minoru
Published: March 2021

The spatiotemporal learning rule (STLR) proposed based on hippocampal neurophysiological experiments is essentially different from the Hebbian learning rule (HEBLR) in terms of the self-organization mechanism. The difference is the self-organization of information from the external world by firing (HEBLR) or not firing (STLR) output neurons. Here, we describe the differences of the self-organization mechanism between the two learning rules by simulating neural network models trained on relatively similar spatiotemporal context information. Comparing the weight distributions after training, the HEBLR shows a unimodal distribution near the training vector, whereas the STLR shows a multimodal distribution. We analyzed the shape of the weight distribution in response to temporal changes in contextual information and found that the HEBLR does not change the shape of the weight distribution for time-varying spatiotemporal contextual information, whereas the STLR is sensitive to slight differences in spatiotemporal contexts and produces a multimodal distribution. These results suggest a critical difference in the dynamic change of synaptic weight distributions between the HEBLR and STLR in contextual learning. They also capture the characteristics of the pattern completion in the HEBLR and the pattern discrimination in the STLR, which adequately explain the self-organization mechanism of contextual information learning.
Unraveling Heterogeneity of Tumor Cells and Microenvironment and Its Clinical Implications for Triple Negative Breast Cancer
Authors: Jiang Ke , Dong Mengting , Li Chunyang , Sheng Jiayu
Published: March 2021

Objective: Triple negative breast cancer (TNBC) is an aggressive subtype of breast cancer, characterized by extensive intratumoral heterogeneity. We aimed to systematically characterize the tumor heterogeneity of TNBC.

Methods: Single-cell RNA sequencing (scRNA-seq) of TNBC cells were obtained from the GSE118389 and GSE75688 datasets. After integration of the two datasets, cell clustering analysis was performed using the Seurat package. According to the marker genes of cell cycle, cell cycle of each cell cluster was determined. Then, function enrichment analysis of marker genes in each cell cluster was performed, followed by ligand–receptor signaling network analysis. CIBERSORT was used to estimate the proportion of 22 immune cells in each sample based on RNA-seq data of 58 normal adjacent tissues and 101 TNBC tissues. After that, prognostic value of immune cells was assessed.

Results: In the integrated datasets, five cells types including B cells, myeloid cells, stromal cells, T cells, and tumor cells were clustered. Functional enrichment analysis revealed the functional heterogeneity of genes in each cell. Intercellular communication networks were conducted based on ligand–receptor pairs. The heterogeneity in the fractions of 22 immune cells was found in TNBC tissues. Furthermore, there was a significant difference in the fractions of these immune cells between adjacent normal tissues and TNBC tissues. Among them, M2 macrophages and neutrophils were significantly associated with clinical outcomes of TNBC. Moreover, the fractions of T cells CD4 memory resting, monocytes, neutrophils, M1 macrophages, and T cells CD4 memory activated were significantly correlated with clinical characteristics of TNBC. As shown in PCA results, these immune cells could significantly distinguish TNBC tissues into adjacent normal tissues.

Conclusion: Our findings characterized the tumor heterogeneity of TNBC, which deepened the understanding of the complex interactions between tumor cells and their microenvironment, especially immune cells.
Understanding Sources of Variation to Improve the Reproducibility of Radiomics
Authors: Zhao Binsheng
Published: March 2021

Radiomics is the method of choice for investigating the association between cancer imaging phenotype, cancer genotype and clinical outcome prediction in the era of precision medicine. The fast dispersal of this new methodology has benefited from the existing advances of the core technologies involved in radiomics workflow: image acquisition, tumor segmentation, feature extraction and machine learning. However, despite the rapidly increasing body of publications, there is no real clinical use of a developed radiomics signature so far. Reasons are multifaceted. One of the major challenges is the lack of reproducibility and generalizability of the reported radiomics signatures (features and models). Sources of variation exist in each step of the workflow; some are controllable or can be controlled to certain degrees, while others are uncontrollable or even unknown. Insufficient transparency in reporting radiomics studies further prevents translation of the developed radiomics signatures from the bench to the bedside. This review article first addresses sources of variation, which is illustrated using demonstrative examples. Then, it reviews a number of published studies and progresses made to date in the investigation and improvement of feature reproducibility and model performance. Lastly, it discusses potential strategies and practical considerations to reduce feature variability and improve the quality of radiomics study. This review focuses on CT image acquisition, tumor segmentation, quantitative feature extraction, and the disease of lung cancer.
Glycolysis and Fatty Acid Oxidation Inhibition Improves Survival in Glioblastoma
Authors: McKelvey Kelly J. , Wilson Erica B. , Short Susan , Melcher Alan A. , Biggs Michael , Diakos Connie I. , Howell Viive M.
Published: March 2021

Glioblastoma (GBM) is the most aggressive adult glioma with a median survival of 14 months. While standard treatments (safe maximal resection, radiation, and temozolomide chemotherapy) have increased the median survival in favorable O(6)-methylguanine-DNA methyltransferase (MGMT)-methylated GBM (~21 months), a large proportion of patients experience a highly debilitating and rapidly fatal disease. This study examined GBM cellular energetic pathways and blockade using repurposed drugs: the glycolytic inhibitor, namely dicholoroacetate (DCA), and the partial fatty acid oxidation (FAO) inhibitor, namely ranolazine (Rano). Gene expression data show that GBM subtypes have similar glucose and FAO pathways, and GBM tumors have significant upregulation of enzymes in both pathways, compared to normal brain tissue (p < 0.01). DCA and the DCA/Rano combination showed reduced colony-forming activity of GBM and increased oxidative stress, DNA damage, autophagy, and apoptosis in vitro. In the orthotopic Gl261 and CT2A syngeneic murine models of GBM, DCA, Rano, and DCA/Rano increased median survival and induced focal tumor necrosis and hemorrhage. In conclusion, dual targeting of glycolytic and FAO metabolic pathways provides a viable treatment that warrants further investigation concurrently or as an adjuvant to standard chemoradiation for GBM.
MACC1 Is Associated With Epithelial–Mesenchymal Transition and Can Predict Poor Prognosis in Nasopharyngeal Carcinoma
Authors: Cheng Hao , Zhou Linxiang , Long Yalan , Xiang Juanjuan , Chen Longhua
Published: March 2021

Background

Given the reported correlation between the oncogene metastasis-associated in colon cancer 1 (MACC1) and nasopharyngeal carcinoma (NPC), as well as between MACC1 and epithelial–mesenchymal transition (EMT), we speculated that EMT is a likely causative link between MACC1 expression and poor NPC prognosis. Thus, we aim to clarify the relationship between MACC1 and EMT in NPC prognosis.

Material and Methods

We performed immunohistochemical examination of tissue sections from 128 NPC patients that were divided into six groups corresponding to high and low protein expression of MACC1 and two EMT-related proteins, vimentin and E-cadherin, and Kaplan–Meier (KM) survival analyses were performed.

Results

KM survival analysis showed that upregulation of MACC1 and vimentin and downregulation of E-cadherin were significantly associated with reduced survival in NPC. Short hairpin RNA (shRNA) interference and immunoblotting in the NPC cell line HNE-1 led to increased E-cadherin but decreased vimentin levels. MACC1 overexpression was significantly correlated with poor 5-year overall survival, metastasis-free survival, and disease-free survival (P<0.05) but not with poor relapse-free survival (P>0.05). Univariate analyses revealed that MACC1, E-cadherin, and vimentin levels along with T and N tumor classifications and cancer staging are significant prognostic factors of NPC (P<0.05).

Conclusion

Our findings showed the association between MACC1 and EMT in NPC malignancy and support the role of MACC1 as a prognostic biomarker and molecular target for NPC treatment.
Case Report: Transarterial Chemoembolization in Combination With Tislelizumab Downstages Unresectable Hepatocellular Carcinoma Followed by Radical Salvage Resection
Authors: Chao Jiashuo , Zhu Qi , Chen Desheng , An Xiao , Liu Aiqun , Zhou Fei , Yuan Lin , Wang Zhaowen , Sun Hongcheng
Published: March 2021

Introduction

Transarterial chemoembolization (TACE) is inefficient at converting unresectable hepatocellular carcinoma (uHCC) to resectable. Treatment with immune checkpoint inhibitors (ICIs) is an emerging strategy for uHCC. Combined therapy of TACE with ICIs is considered to improve the therapeutic effect.

Case presentation

A 45-year-old man was diagnosed with a bulky HCC under cirrhotic background without distant metastasis. Curative resection was infeasible, and TACE plus tislelizumab (an ICI targeting PD-1) was applied. The treatment course, starting from TACE and followed by tislelizumab one week later, was repeated every four weeks. After three courses, the tumor showed striking shrink in volume with complete radiological response, which permitted salvage resection. Notably, pathological examination found complete necrosis of the tumor with massive infiltration of lymphocytes in the tumor-nontumor interface and extensive granulomatous inflammation in the surrounding nontumor liver, indicating activated immune response synergistically caused by TACE with tislelizumab. The patient is now living well without tumor recurrence for 6 months after surgery.

Conclusion

TACE in combination with tislelizumab may represent a potent strategy for uHCC. Data from randomized clinical trials are needed to assess its safety and effect in the setting of preoperative downstaging therapy.
Mechanisms and Efficacy of Chinese Herbal Medicines in Chronic Kidney Disease
Authors: Zhao Mingming , Yu Yi , Wang Rumeng , Chang Meiying , Ma Sijia , Qu Hua , Zhang Yu
Published: March 2021

As the current treatment of chronic kidney disease (CKD) is limited, it is necessary to seek more effective and safer treatment methods, such as Chinese herbal medicines (CHMs). In order to clarify the modern theoretical basis and molecular mechanisms of CHMs, we reviewed the knowledge based on publications in peer-reviewed English-language journals, focusing on the anti-inflammatory, antioxidative, anti-apoptotic, autophagy-mediated and antifibrotic effects of CHMs commonly used in kidney disease. We also discussed recently published clinical trials and meta-analyses in this field. Based on recent studies regarding the mechanisms of kidney disease in vivo and in vitro, CHMs have anti-inflammatory, antioxidative, anti-apoptotic, autophagy-mediated, and antifibrotic effects. Several well-designed randomized controlled trials (RCTs) and meta-analyses demonstrated that the use of CHMs as an adjuvant to conventional medicines may benefit patients with CKD. Unknown active ingredients, low quality and small sample sizes of some clinical trials, and the safety of CHMs have restricted the development of CHMs. CHMs is a potential method in the treatment of CKD. Further study on the mechanism and well-conducted RCTs are urgently needed to evaluate the efficacy and safety of CHMs.
Anthracycline Induced Cardiac Disorders in Childhood Acute Lymphoblastic Leukemia: A Single-Centre, Retrospective, Observational Study
Authors: Yu Hui , Qiu Yining , Yu Hui , Wang Zhujun , Xu Jiawei , Peng Yun , Wan Xia , Wu Xiaoyan , Jin Runming , Zhou Fen
Published: March 2021

Anthracycline-associated cardiotoxicity is frequently seen in cancer survivors years after treatment, but it is rare in patients on chemotherapy. This study aimed to investigate the clinical characteristics of cardiac disorders in children with acute lymphoblastic leukemia (ALL) during chemotherapy. A retrospective case study was conducted in children with ALL, for whom electrocardiogram (ECG) and echocardiography (Echo) were regularly assessed before each course of chemotherapy. The cardiac disorders were diagnosed according to the Common Terminology Criteria for Adverse Events (CTCAE) Version 5.0. Binary logistic regression analysis was used to identify risk factors associated with cardiac disorders. There were 171 children eligible for the study, and 78 patients (45.61%) were confirmed as having cardiac disorders. The incidence of cardiac disorders was dependent upon the cumulative dose of daunorubicin (DNR) (p = 0.030, OR = 1.553, 95% CI: 1.005–3.108). Four patients (2.34%) presented with palpitation, chest pain, and persistent tachycardia, and they were cured or improved after medical intervention. A total of 74 patients (43.27%) had subclinical cardiac disorders confirmed by ECG or Echo. ECG abnormalities were commonly seen in the induction and continuation treatments, including arrhythmias (26, 15.20%), ST changes (24, 14.04%) and conduction disorders (4, 2.34%). Pericardial effusion (14, 8.19%), left ventricular hypertrophy (11, 6.43%), a widened pulmonary artery (5, 2.92%) and valvular insufficiency (5, 2.92%) suggested by Echo occurred after induction chemotherapy. Therefore, cardiac disorders with clinical manifestations are rare and need early intervention. Subclinical cardiac disorders are common but very hidden in children during ALL chemotherapy. Regular ECG and Echo could help paediatricians to identify and monitor patients with asymptomatic cardiac disorders earlier.
Mahuang Decoction Antagonizes Acute Liver Failure via Modulating Tricarboxylic Acid Cycle and Amino Acids Metabolism
Authors: Liao Wenting , Jin Qiwen , Liu Junning , Ruan Yiling , Li Xinran , Shen Yueyue , Zhang Zhicheng , Wang Yong , Wu Shengming , Zhang Junying , Kang Lifeng , Wu Chunyong
Published: March 2021

Acute liver failure (ALF) is a serious clinical disorder with high fatality rates. Mahuang decoction (MHD), a well-known traditional Chinese medicine, has multiple pharmacological effects, such as anti-inflammation, anti-allergy, anti-asthma, and anti-hyperglycemia. In this study, we investigated the protective effect of MHD against ALF. In the lipopolysaccharide and D-galactosamine (LPS/D-GalN)-induced ALF mouse model, the elevated activities of the serum alanine and aspartate transaminases as well as the liver pathological damage were markedly alleviated by MHD. Subsequently, a metabolomics study based on the ultrahigh performance liquid chromatograph coupled with Q Exactive Orbitrap mass spectrometry was carried to clarify the therapeutic mechanisms of MHD against ALF. A total of 36 metabolites contributing to LPS/D-GalN-induced ALF were identified in the serum samples, among which the abnormalities of 27 metabolites were ameliorated by MHD. The analysis of metabolic pathways revealed that the therapeutic effects of MHD are likely due to the modulation of the metabolic disorders of tricarboxylic acid (TCA) cycle, retinol metabolism, tryptophan metabolism, arginine and proline metabolism, nicotinate and nicotinamide metabolism, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan synthesis, as well as cysteine and methionine metabolism. This study demonstrated for the first time that MHD exerted an obvious protective effect against ALF mainly through the regulation of TCA cycle and amino acid metabolism, highlighting the importance of metabolomics to investigate the drug-targeted metabolic pathways.
New Modalities of 3D Pluripotent Stem Cell-Based Assays in Cardiovascular Toxicity
Authors: Orsolits Barbara , Kovács Zsófia , Kriston-Vizi János , Merkely Béla , Földes Gábor
Published: March 2021

The substantial progress of the human induced pluripotent stem cell (hiPSC) technologies over the last decade has provided us with new opportunities for cardiovascular drug discovery, regenerative medicine, and disease modeling. The combination of hiPSC with 3D culture techniques offers numerous advantages for generating and studying physiological and pathophysiological cardiac models. Cells grown in 3D can overcome many limitations of 2D cell cultures and animal models. Furthermore, it enables the investigation in an architecturally appropriate, complex cellular environment in vitro. Yet, generation and study of cardiac organoids—which may contain versatile cardiovascular cell types differentiated from hiPSC—remain a challenge. The large-scale and high-throughput applications require accurate and standardised models with highly automated processes in culturing, imaging and data collection. Besides the compound spatial structure of organoids, their biological processes also possess different temporal dynamics which require other methods and technologies to detect them. In this review, we summarise the possibilities and challenges of acquiring relevant information from 3D cardiovascular models. We focus on the opportunities during different time-scale processes in dynamic pharmacological experiments and discuss the putative steps toward one-size-fits-all assays.
Association Between NR3C1 Mutations and Glucocorticoid Resistance in Children With Acute Lymphoblastic Leukemia
Authors: Liu Haiyan , Li Ziping , Qiu Fei , Li Chunjie , Lin Xiaojing , He Yingyi , Qian Maoxiang , Song Yuanbin , Zhang Hui
Published: March 2021

Treatment outcomes in children with acute lymphoblastic leukemia (ALL) have been improved substantially, with a cure rate exceeding 80% using conventional therapy. However, the outcome for patients with relapsed/refractory ALL remains unsatisfactory, despite the fact that these patients generally receive more intense therapy. Glucocorticoid (GC) resistance is a leading cause of treatment failure and relapse in ALL. Abnormal NR3C1 transcription and/or translation is strongly associated with GC resistance, but the underlying molecular mechanism and the clinical value of NR3C1 alterations with GC resistance in ALL treatment remain unclear. This study applied panel sequencing to 333 newly diagnosed and 18 relapsed ALL samples to characterize the link between NR3C1 and ALL further. We identified NR3C1 mutations in three patients with newly diagnosed ALL (0.9%) and two patients with relapsed ALL (11.1%). Functional analyses revealed that four of these five NR3C1 mutations (p. R477H, p. Y478C, p. P530fs, and p. H726P) were loss-of-function (LoF) mutations. A drug sensitivity test further showed that LoF NR3C1 mutations influence GC resistance. Saturated mutagenesis of hotspot R477 demonstrated the importance of this residue for NR3C1 function. The dominant-negative effect of p. R477C and p. R477S and the non-dominant negative effect of p. R477H and p. Y478C suggests multiple mechanisms underlying GC resistance. Thus, primary or acquired genomic lesions in NR3C1 may play a critical role in GC resistance and contribute to ALL treatment failure and/or relapse.