bluuebunny/crossref_metadata_2025 huggingface dataset:
Analysis of Salivary Metabolites by Nuclear Magnetic Resonance Before and After Oral Mucosa Cleaning of Infants in the Pre-dental Period
Authors: Letieri Aline dos Santos , Freitas-Fernandes Liana Bastos , Albarello Lourenço Luís , Fontes Gabriela Pereira , de Souza Ivete Pomarico Ribeiro , Valente Ana Paula , Fidalgo Tatiana Kelly da Silva
Published: June 2021

The aim of the present study was to verify if a protocol for cleaning the oral cavity of infants in the pre-dental period can reduce extrinsic salivary metabolites observed through Nuclear Magnetic Resonance (NMR). A cross-sectional clinical study with a convenience sample was conducted, and infants were recruited at the UFRJ Pediatric Dentistry Clinic. Participants who had used antibiotics and/or antifungals up to 3 months before and whose legal guardians did not consent or sign the Informed Consent Form were excluded. An anamnesis was performed with the guardians and the participants' intraoral clinical examination. Initial collection of unstimulated total saliva was performed using an automatic pipette with sterile plastic tips in the buccal floor region, at least 1 h after the last feeding. Subsequently, the infants' oral mucosa was cleaned with gauze moistened with filtered water, and after 5 min, a new collection was performed, using the same methodology. The obtained samples were immediately transferred on ice to the laboratory, centrifuged (10,000 g), and stored at −80°C. The NMR analyses were performed using a 500-MHz spectrometer Bruker, Germany); evaluations were done via the 1H and 1H-1H TOCSY spectra for metabolite signaling. Eleven pre-dental infants were evaluated, with a mean age of 3.8 months, including six girls (55%). Of these, nine participants (82%) were exclusively breastfed. The higher presence of components such as lactose, glucose, sugars, acetate, alanine, and lactate were observed in the samples before oral mucosa cleaning. Regarding the type of diet, more lactose was observed in the saliva of patients who were exclusively breastfed than those that received mixed feeding. We conclude that the oral mucosa cleaning of infants in the pre-dental period tends to reduce the concentration of extrinsic components from the diet, such as lactose, in the salivary metabolomic profile analyzed by NMR.
Ice Cliff Dynamics of Debris-Covered Trakarding Glacier in the Rolwaling Region, Nepal Himalaya
Authors: Sato Yota , Fujita Koji , Inoue Hiroshi , Sunako Sojiro , Sakai Akiko , Tsushima Akane , Podolskiy Evgeny A. , Kayastha Rakesh , Kayastha Rijan B.
Published: June 2021

Ice cliffs can act as “hot spots” for melt on debris-covered glaciers and promote local glacier mass loss. Repeat high-resolution remote-sensing data are therefore required to monitor the role of ice cliff dynamics in glacier mass loss. Here we analyze high-resolution aerial photogrammetry data acquired during the 2007, 2018, and 2019 post-monsoon seasons to delineate and monitor the morphology, distribution, and temporal changes of the ice cliffs across the debris-covered Trakarding Glacier in the eastern Nepal Himalaya. We generate an ice cliff inventory from the 2018 and 2019 precise terrain data, with ice cliffs accounting for 4.7 and 6.1% of the debris-covered area, respectively. We observe large surface lowering (>2.0 m a−1) where there is a denser distribution of ice cliffs. We also track the survival, formation, and disappearance of ice cliffs from 2018 to 2019, and find that ∼15% of the total ice cliff area is replaced by new ice cliffs. Furthermore, we observe the overall predominance of northwest-facing ice cliffs, although we do observe spatial heterogeneities in the aspect variance of the ice cliffs (ice cliffs face in similar/various directions). Many new ice cliffs formed across the stagnant middle sections of the glacier, coincident with surface water drainage and englacial conduit intake observations. This spatial relationship between ice cliffs and the glacier hydrological system suggests that these englacial and supraglacial hydrological systems play a significant role in ice cliff formation.
Insulin-Like Growth Factor Pathway and the Thyroid
Authors: Smith Terry J.
Published: June 2021

The insulin-like growth factor (IGF) pathway comprises two activating ligands (IGF-I and IGF-II), two cell-surface receptors (IGF-IR and IGF-IIR), six IGF binding proteins (IGFBP) and nine IGFBP related proteins. IGF-I and the IGF-IR share substantial structural and functional similarities to those of insulin and its receptor. IGF-I plays important regulatory roles in the development, growth, and function of many human tissues. Its pathway intersects with those mediating the actions of many cytokines, growth factors and hormones. Among these, IGFs impact the thyroid and the hormones that it generates. Further, thyroid hormones and thyrotropin (TSH) can influence the biological effects of growth hormone and IGF-I on target tissues. The consequences of this two-way interplay can be far-reaching on many metabolic and immunologic processes. Specifically, IGF-I supports normal function, volume and hormone synthesis of the thyroid gland. Some of these effects are mediated through enhancement of sensitivity to the actions of TSH while others may be independent of pituitary function. IGF-I also participates in pathological conditions of the thyroid, including benign enlargement and tumorigenesis, such as those occurring in acromegaly. With regard to Graves’ disease (GD) and the periocular process frequently associated with it, namely thyroid-associated ophthalmopathy (TAO), IGF-IR has been found overexpressed in orbital connective tissues, T and B cells in GD and TAO. Autoantibodies of the IgG class are generated in patients with GD that bind to IGF-IR and initiate the signaling from the TSHR/IGF-IR physical and functional protein complex. Further, inhibition of IGF-IR with monoclonal antibody inhibitors can attenuate signaling from either TSHR or IGF-IR. Based on those findings, the development of teprotumumab, a β-arrestin biased agonist as a therapeutic has resulted in the first medication approved by the US FDA for the treatment of TAO. Teprotumumab is now in wide clinical use in North America.
The Application of PMA (Propidium Monoazide) to Different Target Sequence Lengths of Zebrafish eDNA: A New Approach Aimed Toward Improving Environmental DNA Ecology and Biological Surveillance
Authors: Hirohara Takaya , Tsuri Kenji , Miyagawa Koichi , Paine Robert T. R. , Yamanaka Hiroki
Published: June 2021

Environmental DNA (eDNA) analysis has enabled more sensitive and efficient biological monitoring than traditional methods. However, since the target species is not directly observed, interpretation of results cannot preclude process Type I errors. Specifically, there may be a spatial or temporal gap between the target eDNA and the eDNA source in the sampled area. Moreover, eDNA surveillance lacks the ability to distinguish whether eDNA originated from a living or non-living source. This kind of Type I error is difficult to control for, in part, because the relationship between the state of eDNA (i.e., intracellular or extracellular) and the degradation rate is still unclear. Here, we applied PMA (Propidium monoazide) to eDNA analysis which enabled us to differentiate “intact cells” from “disrupted cells.” PMA is a dye that has a high affinity for double-stranded DNA and forms a covalent bond with double-stranded DNA and inhibits amplification of the bonded DNA molecules by PCR. Since PMA is impermeable to the cell membrane, DNA protected by an intact cell membrane can be selectively detected. In this study, we investigated the workability of PMA on vertebrate eDNA using zebrafish, Danio rerio. Aquarium water was incubated for 1 week to monitor the eDNA degradation process of both intracellular and extracellular eDNA. We developed ten species-specific quantitative PCR assays for D. rerio with different amplification lengths that enabled independent quantification of total eDNA (sum of intracellular and extracellular eDNA, commonly measured in other studies) and intracellular eDNA (DNA in intact cells) and allow for analyses of sequence length-dependent eDNA degradation in combination with PMA. We confirmed that PMA is effective at differentiating “intact” and “disrupted” fish cells. We found that total eDNA and intracellular eDNA have different degradation processes that are dependent on the length of target sequence. For future conservation efforts using eDNA analyses, it is necessary to increase the reliability of the analysis results. The research presented here provides new analysis tools that expand our understanding of the ecology of eDNA, so that more accurate and reliable conclusions can be determined.
Gene Expression Modification by an Autosomal Inversion Associated With Three Male Mating Morphs
Authors: Loveland Jasmine L. , Lank David B. , Küpper Clemens
Published: June 2021

Chromosomal inversions are structural rearrangements that frequently provide genomic substrate for phenotypic diversity. In the ruff Philomachus pugnax, three distinct male reproductive morphs (Independents, Satellites and Faeders) are genetically determined by a 4.5 Mb autosomal inversion. Here we test how this stable inversion polymorphism affects gene expression in males during the lekking season. Gene expression may be altered through disruptions at the breakpoints and the accumulation of mutations due to suppressed recombination. We used quantitative PCR to measure expression of 11 candidate inversion genes across three different tissues (liver, adrenal glands and gonads) and tested for allelic imbalance in four inversion genes across 12 males of all three morphs (8 Independents, 2 Satellites, 2 Faeders). We quantified transcripts of CENPN, an essential gene disrupted by the inversion at the proximal breakpoint, at different exons distributed near and across the breakpoint region. Consistent with dosage dependent gene expression for the breakpoint gene CENPN, we found that expression in Independents was broadly similar for transcripts segments from inside and outside the inversion regions, whereas for Satellites and Faeders, transcript segments outside of the inversion showed at least twofold higher expression than those spanning over the breakpoint. Within the inversion, observed expression differences for inversion males across all four genes with allele-specific primers were consistent with allelic imbalance. We further analyzed gonadal expression of two inversion genes, HSD17B2 and SDR42E1, along with 12 non-inversion genes related to steroid metabolism and signaling in 25 males (13 Independents, 7 Satellites, 5 Faeders). Although we did not find clear morph differentiation for many individual genes, all three morphs could be separated based on gene expression differences when using linear discriminant analysis (LDA), regardless of genomic location (i.e., inside or outside of the inversion). This was robust to the removal of genes with the highest loadings. Pairwise correlations in the expression of genes showed significant correlations for 9–18 pairs of genes within morphs. However, between morphs, we only found a single association between genes SDR42E1 and AROM for Independents and Satellites. Our results suggest complex and wide-ranging changes in gene expression caused by structural variants.
Construction and Analysis of the Dysregulated ceRNA Network and Identification of Risk Long Noncoding RNAs in Breast Cancer
Authors: Su Xiaojie , Yu Zhaoyan , Zhang Yuexin , Chen Jiaxin , Wei Ling , Sun Liang
Published: June 2021

Breast cancer (BRCA) is the second leading cause of cancer-related mortality in women worldwide. However, the molecular mechanism involved in the development of BRCA is not fully understood. In this study, based on the miRNA-mediated long non-coding RNA (lncRNA)–protein coding gene (PCG) relationship and lncRNA–PCG co-expression information, we constructed and analyzed a specific dysregulated lncRNA–PCG co-expression network in BRCA. Then, we performed the random walk with restart (RWR) method to prioritize BRCA-related lncRNAs through comparing their RWR score and significance. As a result, we identified 30 risk lncRNAs for BRCA, which can distinguish normal and tumor samples. Moreover, through gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis, we found that these risk lncRNAs mainly synergistically exerted functions related to cell cycle and DNA separation and replication. At last, we developed a four-lncRNA prognostic signature (including AP000851.1, LINC01977, MAFG-DT, SIAH2-AS1) and assessed the survival accuracy of the signature by performing time-dependent receiver operating characteristic (ROC) analysis. The areas under the ROC curve for 1, 3, 5, and 10 years of survival prediction were 0.68, 0.61, 0.62, and 0.63, respectively. The multivariable Cox regression results verified that the four-lncRNA signature could be used as an independent prognostic biomarker in BRCA. In summary, these results have important reference value for the study of diagnosis, treatment, and prognosis evaluation of BRCA.
Amino Acid Trp: The Far Out Impacts of Host and Commensal Tryptophan Metabolism
Authors: Grifka-Walk Heather M. , Jenkins Brittany R. , Kominsky Douglas J.
Published: June 2021

Tryptophan (Trp) is an essential amino acid primarily derived from the diet for use by the host for protein synthesis. The intestinal tract is lined with cells, both host and microbial, that uptake and metabolize Trp to also generate important signaling molecules. Serotonin (5-HT), kynurenine and its downstream metabolites, and to a lesser extent other neurotransmitters are generated by the host to signal onto host receptors and elicit physiological effects. 5-HT production by neurons in the CNS regulates sleep, mood, and appetite; 5-HT production in the intestinal tract by enterochromaffin cells regulates gastric motility and inflammation in the periphery. Kynurenine can signal onto the aryl hydrocarbon receptor (AHR) to elicit pleiotropic responses from several cell types including epithelial and immune cells, or can be further metabolized into bioactive molecules to influence neurodegenerative disease. There is a remarkable amount of cross-talk with the microbiome with regard to tryptophan metabolites as well. The gut microbiome can regulate the production of host tryptophan metabolites and can use dietary or recycled trp to generate bioactive metabolites themselves. Trp derivatives like indole are able to signal onto xenobiotic receptors, including AHR, to elicit tolerogenic effects. Here, we review studies that demonstrate that tryptophan represents a key intra-kingdom signaling molecule.
CD3+CD4+gp130+ T Cells Are Associated With Worse Disease Activity in Systemic Lupus Erythematosus Patients
Authors: Mohd Shukri Nur Diyana , Farah Izati Aziz , Wan Ghazali Wan Syamimee , Che Hussin Che Maraina , Wong Kah Keng
Published: June 2021

The receptors for IL-35, IL-12Rβ2 and gp130, have been implicated in the inflammatory pathophysiology of autoimmune diseases. In this study, we set out to investigate the serum IL-35 levels and the surface levels of IL-12Rβ2 and gp130 in CD3+CD4+, CD3+CD4─ and CD3─CD4─ lymphocyte subpopulations in systemic lupus erythematosus (SLE) patients (n=50) versus healthy controls (n=50). The potential T cell subsets associated with gp130 transcript (i.e. IL6ST) expression in CD4+ T cells of SLE patients was also examined in publicly-available gene expression profiling (GEP) datasets. Here, we report that serum IL-35 levels were significantly higher in SLE patients than healthy controls (p=0.038) but it was not associated with SLEDAI-2K scores. The proportions of IL-12Rβ2+ and gp130+ cells in SLE patients did not differ significantly with those of healthy controls in all lymphocyte subpopulations investigated. Essentially, higher SLEDAI-2K scores were positively correlated with increased proportion of gp130+ cells, but not IL-12Rβ2+ cells, on CD3+CD4+ T cells (r=0.425, p=0.002, q=0.016). Gene Set Enrichment Analysis (GSEA) of a GEP dataset of CD4+ T cells isolated from SLE patients (n=8; GSE4588) showed that IL6ST expression was positively associated with genes upregulated in CD4+ T cells vs myeloid or B cells (q<0.001). In an independent GEP dataset of CD4+ T cells isolated from SLE patients (n=9; GSE1057), IL6ST expression was induced upon anti-CD3 stimulation, and that Treg, TCM and CCR7+ T cells gene sets were significantly enriched (q<0.05) by genes highly correlated with IL6ST expression (n=92 genes; r>0.75 with IL6ST expression) upon anti-CD3 stimulation in these SLE patients. In conclusion, gp130 signaling in CD3+CD4+ T cell subsets may contribute to increased disease activity in SLE patients, and it represents a promising therapeutic target for inhibition in the disease.
Immunomodulatory Effects of Mesenchymal Stem Cells on Drug-Induced Acute Kidney Injury
Authors: Han Qiuxia , Wang Xiaochen , Ding Xiaonan , He Jun , Cai Guangyan , Zhu Hanyu
Published: June 2021

Drug-induced nephrotoxicity is an important and increasing cause of acute kidney injury (AKI), which accounts for approximately 20% of hospitalized patients. Previous reviews studies on immunity and AKI focused mainly on ischemia-reperfusion (IR), whereas no systematic review addressing drug-induced AKI and its related immune mechanisms is available. Recent studies have provided a deeper understanding on the mechanisms of drug-induced AKI, among which acute tubular interstitial injury induced by the breakdown of innate immunity was reported to play an important role. Emerging research on mesenchymal stem cell (MSC) therapy has revealed its potential as treatment for drug-induced AKI. MSCs can inhibit kidney damage by regulating the innate immune balance, promoting kidney repair, and preventing kidney fibrosis. However, it is important to note that there are various sources of MSCs, which impacts on the immunomodulatory ability of the cells. This review aims to address the immune pathogenesis of drug-induced AKI versus that of IR-induced AKI, and to explore the immunomodulatory effects and therapeutic potential of MSCs for drug-induced AKI.
Raising the ‘Good’ Oxidants for Immune Protection
Authors: Dumas Alexia , Knaus Ulla G.
Published: June 2021

Redox medicine is a new therapeutic concept targeting reactive oxygen species (ROS) and secondary reaction products for health benefit. The concomitant function of ROS as intracellular second messengers and extracellular mediators governing physiological redox signaling, and as damaging radicals instigating or perpetuating various pathophysiological conditions will require selective strategies for therapeutic intervention. In addition, the reactivity and quantity of the oxidant species generated, its source and cellular location in a defined disease context need to be considered to achieve the desired outcome. In inflammatory diseases associated with oxidative damage and tissue injury, ROS source specific inhibitors may provide more benefit than generalized removal of ROS. Contemporary approaches in immunity will also include the preservation or even elevation of certain oxygen metabolites to restore or improve ROS driven physiological functions including more effective redox signaling and cell-microenvironment communication, and to induce mucosal barrier integrity, eubiosis and repair processes. Increasing oxidants by host-directed immunomodulation or by exogenous supplementation seems especially promising for improving host defense. Here, we summarize examples of beneficial ROS in immune homeostasis, infection, and acute inflammatory disease, and address emerging therapeutic strategies for ROS augmentation to induce and strengthen protective host immunity.
The Role of Dysbiosis in Critically Ill Patients With COVID-19 and Acute Respiratory Distress Syndrome
Authors: Battaglini Denise , Robba Chiara , Fedele Andrea , Trancǎ Sebastian , Sukkar Samir Giuseppe , Di Pilato Vincenzo , Bassetti Matteo , Giacobbe Daniele Roberto , Vena Antonio , Patroniti Nicolò , Ball Lorenzo , Brunetti Iole , Torres Martí Antoni , Rocco Patricia Rieken Macedo , Pelosi Paolo
Published: June 2021

In late December 2019, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) quickly spread worldwide, and the syndrome it causes, coronavirus disease 2019 (COVID-19), has reached pandemic proportions. Around 30% of patients with COVID-19 experience severe respiratory distress and are admitted to the intensive care unit for comprehensive critical care. Patients with COVID-19 often present an enhanced immune response with a hyperinflammatory state characterized by a “cytokine storm,” which may reflect changes in the microbiota composition. Moreover, the evolution to acute respiratory distress syndrome (ARDS) may increase the severity of COVID-19 and related dysbiosis. During critical illness, the multitude of therapies administered, including antibiotics, sedatives, analgesics, body position, invasive mechanical ventilation, and nutritional support, may enhance the inflammatory response and alter the balance of patients' microbiota. This status of dysbiosis may lead to hyper vulnerability in patients and an inappropriate response to critical circumstances. In this context, the aim of our narrative review is to provide an overview of possible interaction between patients' microbiota dysbiosis and clinical status of severe COVID-19 with ARDS, taking into consideration the characteristic hyperinflammatory state of this condition, respiratory distress, and provide an overview on possible nutritional strategies for critically ill patients with COVID-19-ARDS.
Genomic and Chemical Investigation of Bioactive Secondary Metabolites From a Marine-Derived Fungus Penicillium steckii P2648
Authors: Yao Guangshan , Chen Xiaofeng , Zheng Huawei , Liao Danhua , Yu Zhi , Wang Zonghua , Chen Jianming
Published: June 2021

Marine fungi of the genus Penicillium are rich resources of secondary metabolites, showing a variety of biological activities. Our anti-bacterial screening revealed that the crude extract from a coral-derived fungus Penicillium steckii P2648 showed strong activity against some pathogenic bacteria. Genome sequencing and mining uncovered that there are 28 secondary metabolite gene clusters in P2648, potentially involved in the biosynthesis of antibacterial compounds. Chemical isolation and structural determination suggested citrinin is the dominant component of the crude extracts of P2648, and our further tests confirmed that citrinin showed excellent activities against various pathogenic bacteria. Moreover, the gene cluster containing a homolog of the polyketide synthase CitS was identified as the citrinin biosynthesis gene cluster through genetic analysis. Interestingly, three isoquinoline alkaloids were unexpectedly activated and isolated from the Δcits mutant and structural determination by using high-resolution electron spray ionization mass spectroscopy (HRESIMS), 1D, and 2D NMR. Further antibacterial assays displayed that compounds 1 and 2, but not compound 3, showed moderate activities against two antibiotic-resistant pathogenic bacteria with minimum inhibitory concentration (MIC) of 16–32 μg/ml. In conclusion, our results demonstrated that citrinin and isoquinoline alkaloids represent as the major antibacterial agents in the coral-associated fungus P. steckii P2648, and our genomic and chemical analyses present evidence in support of P. steckii P2648 as a potent natural products source for anti-bacterial drug discovery.
Complex Interaction Networks Among Cyanolichens of a Tropical Biodiversity Hotspot
Authors: Kaasalainen Ulla , Tuovinen Veera , Mwachala Geoffrey , Pellikka Petri , Rikkinen Jouko
Published: June 2021

Interactions within lichen communities include, in addition to close mutualistic associations between the main partners of specific lichen symbioses, also more elusive relationships between members of a wider symbiotic community. Here, we analyze association patterns of cyanolichen symbionts in the tropical montane forests of Taita Hills, southern Kenya, which is part of the Eastern Afromontane biodiversity hotspot. The cyanolichen specimens analyzed represent 74 mycobiont taxa within the order Peltigerales (Ascomycota), associating with 115 different variants of the photobionts genus Nostoc (Cyanobacteria). Our analysis demonstrates wide sharing of photobionts and reveals the presence of several photobiont-mediated lichen guilds. Over half of all mycobionts share photobionts with other fungal species, often from different genera or even families, while some others are strict specialists and exclusively associate with a single photobiont variant. The most extensive symbiont network involves 24 different fungal species from five genera associating with 38 Nostoc photobionts. The Nostoc photobionts belong to two main groups, the Nephroma-type Nostoc and the Collema/Peltigera-type Nostoc, and nearly all mycobionts associate only with variants of one group. Among the mycobionts, species that produce cephalodia and those without symbiotic propagules tend to be most promiscuous in photobiont choice. The extent of photobiont sharing and the structure of interaction networks differ dramatically between the two major photobiont-mediated guilds, being both more prevalent and nested among Nephroma guild fungi and more compartmentalized among Peltigera guild fungi. This presumably reflects differences in the ecological characteristics and/or requirements of the two main groups of photobionts. The same two groups of Nostoc have previously been identified from many lichens in various lichen-rich ecosystems in different parts of the world, indicating that photobiont sharing between fungal species is an integral part of lichen ecology globally. In many cases, symbiotically dispersing lichens can facilitate the dispersal of sexually reproducing species, promoting establishment and adaptation into new and marginal habitats and thus driving evolutionary diversification.
Metaproteomic Discovery and Characterization of a Novel Lipolytic Enzyme From an Indian Hot Spring
Authors: Sander Dennis , Yu Yanfei , Sukul Premankur , Schäkermann Sina , Bandow Julia E. , Mukherjee Trinetra , Mukhopadhyay Subhra Kanti , Leichert Lars I.
Published: June 2021

Lipolytic enzymes are produced by animals, plants and microorganisms. With their chemo-, regio-, and enantio-specific characteristics, lipolytic enzymes are important biocatalysts useful in several industrial applications. They are widely used in the processing of fats and oils, detergents, food processing, paper and cosmetics production. In this work, we used a new functional metaproteomics approach to screen sediment samples of the Indian Bakreshwar hot spring for novel thermo- and solvent-stable lipolytic enzymes. We were able to identify an enzyme showing favorable characteristics. DS-007 showed high hydrolytic activity with substrates with shorter chain length (C10, significantly less hydrolytic activity was observed. A preference for short chain acyl groups is characteristic for esterases, suggesting that DS-007 is an esterase. Consistent with the high temperature at its site of isolation, DS-007 showed a temperature optimum at 55°C and retained 80% activity even after prolonged exposure to temperatures as high as 60°C. The enzyme showed optimum activity at pH 9.5, with more than 50% of its optimum activity between pH 8.0 and pH 9.5. DS-007 also exhibited tolerance toward organic solvents at a concentration of 1% (v/v). One percent of methanol increased the activity of DS-007 by 40% in comparison to the optimum conditions without solvent. In the presence of 10% methanol, DMSO or isopropanol DS-007 still showed around 50% activity. This data indicates that DS-007 is a temperature- and solvent-stable thermophilic enzyme with reasonable activity even at lower temperatures as well as a catalyst that can be used at a broad range of pH values with an optimum in the alkaline range, showing the adaptation to the habitat’s temperature and alkaline pH.
Waddington’s Landscapes in the Bacterial World
Authors: Sánchez-Romero María A. , Casadesús Josep
Published: June 2021

Conrad Waddington’s epigenetic landscape, a visual metaphor for the development of multicellular organisms, is appropriate to depict the formation of phenotypic variants of bacterial cells. Examples of bacterial differentiation that result in morphological change have been known for decades. In addition, bacterial populations contain phenotypic cell variants that lack morphological change, and the advent of fluorescent protein technology and single-cell analysis has unveiled scores of examples. Cell-specific gene expression patterns can have a random origin or arise as a programmed event. When phenotypic cell-to-cell differences are heritable, bacterial lineages are formed. The mechanisms that transmit epigenetic states to daughter cells can have strikingly different levels of complexity, from the propagation of simple feedback loops to the formation of complex DNA methylation patterns. Game theory predicts that phenotypic heterogeneity can facilitate bacterial adaptation to hostile or unpredictable environments, serving either as a division of labor or as a bet hedging that anticipates future challenges. Experimental observation confirms the existence of both types of strategies in the bacterial world.
Blood Pressure Level Is Associated With Changes in Plasma Aβ1 –40 and Aβ1–42 Levels: A Cross-sectional Study Conducted in the Suburbs of Xi’an, China
Authors: She Meilin , Shang Suhang , Hu Ningwei , Chen Chen , Dang Liangjun , Gao Ling , Wei Shan , Huo Kang , Wang Jingyi , Wang Jin , Qu Qiumin
Published: June 2021

Objectives: Amyloid-β (Aβ) deposition in the brain is the hallmark of Alzheimer’s disease (AD) pathology. Hypertension is a risk factor for AD, but the effects of hypertension on Aβ deposition are not fully determined. Considering peripheral Aβ closely relates to Aβ deposition in the brain, we investigated the relationships between blood pressure (BP) level and plasma Aβ concentrations.

Methods: One-thousand and sixty-nine participants (age above 45) from a village in the suburbs of Xi’an, China were enrolled. Questionnaires and validated Chinese versions of the Mini-Mental State Examination (MMSE) were used to collect information about vascular risk factors and assess cognition function. The apolipoprotein E (ApoE) genotype was detected using PCR and sequencing. Plasma Aβ levels were measured using ELISA. The associations between BP and plasma Aβ levels were analyzed by using multivariate linear regression.

Results: Plasma Aβ1–40 level was higher in high BP group than that in normal BP group (53.34 ± 8.50 pg/ml vs. 51.98 ± 8.96 pg/ml, P = 0.013), in high SBP group than that in normal SBP group (53.68 ± 8.69 pg/ml vs. 51.88 ± 8.80 pg/ml, P = 0.001) and in high MABP group than that in normal MABP group (54.05 ± 8.78 pg/ml vs. 52.04 ± 8.75 pg/ml, P = 0.001). After controlling for the confounding factors, SBP (b = 0.078, P < 0.001), DBP (b = 0.090, P = 0.008) and MABP (b = 0.104, P < 0.001) correlated with plasma Aβ1–40 level positively in ApoE ε4 non-carriers, but not ApoE ε4 carriers.

Conclusions: Elevated BP levels were associated with increased plasma Aβ1–40 levels in middle-aged and elderly ApoE ε4 non-carriers.
Supplementary Effect of Choline Alfoscerate on Speech Recognition in Patients With Age-Related Hearing Loss: A Prospective Study in 34 Patients (57 Ears)
Authors: Na Gina , Kwak Sang Hyun , Jang Seung Hyun , Noh Hye Eun , Kim Jungghi , Yang SeungJoon , Jung Jinsei
Published: June 2021

To investigate the effect of choline alfoscerate (CA) on hearing amplification in patients with age related hearing loss, we performed a prospective case-control observational study from March 2016 to September 2020. We assessed patients with bilateral word recognition score (WRS) <50% using monosyllabic words. The patients were 65–85 years old, without any history of dementia, Alzheimer’s disease, parkinsonism, or depression. After enrollment, all patients started using hearing aids (HA). The CA group received a daily dose of 800 mg CA for 11 months. We performed between-group comparisons of audiological data, including pure tone audiometry, WRS, HA fitting data obtained using real-ear measurement (REM), and the Abbreviated Profile of Hearing Aid benefit scores after treatment. After CA administration, the WRS improved significantly in the CA group (4.2 ± 8.3%), but deteriorated in the control group (−0.6 ± 8.1%, p = 0.035). However, there was no significant between-group difference in the change in pure tone thresholds and aided speech intelligibility index calculated from REM. These findings suggest that the difference in WRS was relevant to central speech understanding rather than peripheral audibility. Therefore, administering oral CA could effectively enrich listening comprehension in older HA users.
Percutaneous Endoscopic Gastrostomy Tube Placement in COVID-19 Patients
Authors: Goyal Hemant , Ali Aman , Bansal Pardeep
Published: June 2021

Intensive care units (ICU) around the world are overburdened with COVID-19 patients with ventilator-dependent chronic respiratory failure (VDRF). Gastroenterology evaluations are being made to address the provision of chronic enteral feeding with the help of percutaneous endoscopic gastrostomy (PEG) placements in these patients. The placement of the PEG tube along with tracheostomy in patients with COVID-19 and prolonged VDRF may expedite discharge planning and increase the availability of ICU beds for other patients. Herein, we describe a multidisciplinary approach of PEG tube placements for patients with SARS-CoV-2-induced chronic VDRF for continued enteral feeding to avoid complications and decrease the length of stay.
Organ Growth and Intestinal Functions of Preterm Pigs Fed Low and High Protein Formulas With or Without Supplemental Leucine or Hydroxymethylbutyrate as Growth Promoters
Authors: Buddington Randal K. , Yakimkova Taisiya , Adebiyi Adebowale , Chizhikov Victor V. , Iskusnykh Igor Y. , Buddington Karyl K.
Published: June 2021

The goal of enteral nutritional support for infants born preterm or small for gestational age (SGA) is to achieve normal growth and development. Yet, this is difficult to achieve because of intestinal immaturity. Our objective was to determine if birth weight, protein intake, and the growth promoters leucine (10 g/L) or calcium-ß-hydroxy-ß-methylbutryate (HMB; 1.1 g/L) would affect trajectories of intestinal growth and functions and weights of other organs. Preterm pigs were delivered at gestational day 105 (91% of term) and fed for 6 or 7 days isocaloric formulas that differed in protein content (50 g or 100 g protein/L), with and without the growth promoters leucine or HMB. For comparative purposes organ weights were measured within 12 h after delivery for six term pigs of low and six of average birth weights. The responses of intestinal growth and total intestinal brush border membrane carbohydrases to protein level and supplemental leucine were of greater magnitude for preterm pigs of lower birth weight. Forskolin stimulated chloride secretion in the proximal small intestine was lower for pigs fed the low protein milk replacers. Capacities of the entire small intestine to transport glucose (mmol/kg-day) were not responsive to protein level, leucine, or HMB, and did not differ between small and large pigs. Relative organ weights of the small and average weight term pigs were similar, but some differed from those of the preterm pigs suggesting preterm birth and the standards of care used for this study altered the trajectories of development for the intestine and other organs. Although leucine is an effective generalized growth promoter that enhances gut development of small preterm pigs, it does not mitigate compromised neurodevelopment. Our findings using preterm pigs as a relevant preclinical model indicate nutrition support strategies can influence development of some gastrointestinal tract characteristics and the growth of other organs.
Low Infiltration of CD8+ PD-L1+ T Cells and M2 Macrophages Predicts Improved Clinical Outcomes After Immune Checkpoint Inhibitor Therapy in Non-Small Cell Lung Carcinoma
Authors: Li Liuning , Lu Guojie , Liu Yang , Gong Longlong , Zheng Xue , Zheng Hongbo , Gu Weiguang , Yang Lin
Published: June 2021

Background

Many clinical studies have shown that patients with non-small cell lung carcinoma (NSCLC) can benefit from immune checkpoint inhibitor (ICI) therapy; however, PD-L1 and tumor mutation burden (TMB), which are recommended by the NCCN guidelines, are still insufficient in predicting the response to and prognosis of immunotherapy. Given the widespread use of ICIs, it is important to find biomarkers that can predict immunotherapy outcomes in NSCLC patients, and the exploration of additional effective biomarkers for ICI therapy is urgently needed.

Methods

A total of 33 stage II-IV NSCLC patients were included in this study. We analyzed immune markers in biopsy and surgical tissue resected from these patients before treatment with ICIs. We examined the infiltration of immune cells and expression of PD-L1 in immune cells using fluorescent multiplex immunohistochemistry (mIHC) stained with CD8/CD68/CD163/PD-L1 antibodies.

Results

In this cohort, we observed that the levels of CD8+ T cells, CD8+PD-L1+ T cells, and CD68+CD163+ M2 macrophages in the total region were independent prognostic factors for progression-free survival (PFS) in NSCLC patients treated with ICIs (HR=0.04, P=0.013; HR=17.70, P=0.026; and HR=17.88, P=0.011, respectively). High infiltration of CD8+ T cells and low infiltration of CD8+PD-L1+ T cells throughout the region were correlated with prolonged PFS (P=0.016 and P=0.02, respectively). No statistically significant difference was observed for CD68+CD163+ M2 macrophages. The joint parameters CD8+ high/CD8+PD-L1+ low, CD8+ high/CD68+CD163+ low and CD8+PD-L1+ low/CD68+CD163+ low predicted better PFS than other joint parameters (P<0.01, P<0.01, and P<0.001, respectively), and they also demonstrated stronger stratification than single biomarkers. The response rate of patients with high infiltration of CD8+ T cells was significantly higher than that of those with low infiltration (P<0.01), and the joint parameters CD8+/CD8+PD-L1+ and CD8+/CD68+CD163+ also demonstrated stronger stratification than single biomarkers.

Conclusions

This retrospective study identified the predictive value of CD8+PD-L1+ T cells, CD8+ T cells, and CD68+CD163+ M2 macrophages in NSCLC patients who received ICIs. Interestingly, our results indicate that the evaluation of joint parameters has certain significance in guiding ICI treatment in NSCLC patients.
Radiomics Analysis of Contrast-Enhanced CT for Hepatocellular Carcinoma Grading
Authors: Chen Wen , Zhang Tao , Xu Lin , Zhao Liang , Liu Huan , Gu Liang Rui , Wang Dai Zhong , Zhang Ming
Published: June 2021

Objectives

To investigate the value of contrast-enhanced computer tomography (CT)-based on radiomics in discriminating high-grade and low-grade hepatocellular carcinoma (HCC) before surgery.

Methods

The retrospective study including 161 consecutive subjects with HCC which was approved by the institutional review board, and the patients were divided into a training group (n = 112) and test group (n = 49) from January 2013 to January 2018. The least absolute shrinkage and selection operator (LASSO) was used to select the most valuable features to build a support vector machine (SVM) model. The performance of the predictive model was evaluated using the area under the curve (AUC), accuracy, sensitivity, and specificity.

Results

The SVM model showed an acceptable ability to differentiate high-grade from low-grade HCC, with an AUC of 0.904 in the training dataset and 0.937 in the test dataset, accuracy (92.2% versus 95.7%), sensitivity(82.5% versus 88.0%), and specificity (92.7% versus 95.8%), respectively.

Conclusion

The machine learning-based radiomics reflects a better evaluating performance in differentiating HCC between low-grade and high-grade, which may contribute to personalized treatment.
Real-World Clinical Outcomes of Biosimilar Trastuzumab (CT-P6) in HER2-Positive Early-Stage and Metastatic Breast Cancer
Authors: Bae Soong June , Kim Jee Hung , Ahn Sung Gwe , Jeung Hei-Cheul , Sohn Joohyuk , Kim Gun Min , Kim Min Hwan , Kim Seung Il , Park Seho , Park Hyung Seok , Kim Ji Ye , Jeong Joon
Published: June 2021

Background

The trastuzumab biosimilar CT-P6 has demonstrated equivalent efficacy and comparable safety to reference trastuzumab (RTZ) in clinical trials of human epidermal growth factor receptor 2 (HER2)-positive early breast cancer (EBC). Here, we present the first real-world comparison of CT-P6 versus RTZ with dual HER2-targeted therapy for the neoadjuvant and palliative first-line treatment with HER2-positive EBC and metastatic breast cancer (MBC) patients in two tertiary hospitals in Korea.

Methods

We retrospectively investigated medical records in the Severance Breast Cancer Registry in Korea. We identified patients with HER2-positive EBC (n=254) who had received neoadjuvant chemotherapy with RTZ or CT-P6, plus pertuzumab, carboplatin and docetaxel (TCHP) and untreated stage IV MBC (n=103) who had received palliative first-line treatment with RTZ or CT-P6, plus pertuzumab and docetaxel (THP) between May 2014 and December 2019. The primary endpoints were pathologic complete response (pCR) in the EBC and progression-free survival (PFS) in the MBC cohort. Overall survival (OS), overall response rate (ORR), disease control rate (DCR), and cardiac safety were secondary endpoints.

Results

A similar percentage of EBC patients achieved a pCR with CT-P6 versus RTZ (74.4% [93/125]) vs 69.8% [90/129], p=0.411). For patients with MBC, median follow-up duration was 23.0 and 41.0 months for CT-P6 and RTZ groups, respectively; median PFS did not differ significantly between two groups (13.0 vs 18.0 months, 95% confidence intervals (CIs) 0.0-26.6 vs 11.3-24.7, p=0.976). The ORR, DCR, and cardiac safety profiles did not also show significant difference efficacy outcomes between two groups.

Conclusions

These real-world data suggest that biosimilar trastuzumab CT-P6 has similar effectiveness and cardiac safety to RTZ in HER2-positive EBC and MBC patients, when administered as part of dual HER2-targeted therapy with pertuzumab plus chemotherapy in the neoadjuvant or palliative setting.
Sex Differences in a Rat Model of Peripheral Neuropathic Pain and Associated Levels of Endogenous Cannabinoid Ligands
Authors: Boullon Laura , Finn David P. , Llorente-Berzal Álvaro
Published: June 2021

Chronic neuropathic pain is a major unmet clinical need affecting 10% of the world population, the majority of whom suffer from co-morbid mood disorders. Sex differences have been reported in pain prevalence, perception and response to analgesics. However, sexual dimorphism in chronic neuropathic pain and the associated neurobiology, are still poorly understood. The lack of efficacy and the adverse effects associated with current pharmacological treatments, further underline the need for new therapeutic targets. The endocannabinoid system (ECS) is a lipid signalling system which regulates a large number of physiological processes, including pain. The aim of this study was to investigate sexual dimorphism in pain-, anxiety- and depression-related behaviours, and concomitant alterations in supraspinal and spinal endocannabinoid levels in the spared nerve injury (SNI) animal model of peripheral neuropathic pain. Sham or SNI surgery was performed in adult male and female Sprague-Dawley rats. Mechanical and cold allodynia was tested weekly using von Frey and acetone drop tests, respectively. Development of depression-related behaviours was analysed using sucrose splash and sucrose preference tests. Locomotor activity and anxiety-related behaviours were assessed with open field and elevated plus maze tests. Levels of endocannabinoid ligands and related N-acylethanolamines in supraspinal regions of the descending inhibitory pain pathway, and spinal cord, were analysed 42 days post-surgery. SNI surgery induced allodynia in rats of both sexes. Female-SNI rats exhibited earlier onset and greater sensitivity to cold and mechanical allodynia than their male counterparts. In male rats, SNI induced a significant reduction of rearing, compared to sham controls. Trends for depressive-like behaviours in females and for anxiety-like behaviours in males were observed after SNI surgery but did not reach statistical significance. No concomitant alterations in levels of endogenous cannabinoid ligands and related N-acylethanolamines were observed in the regions analysed. Our results demonstrate differential development of SNI-induced nociceptive behaviour between male and female rats suggesting important sexually dimorphic modifications in pain pathways. SNI had no effect on depression- or anxiety-related behaviours in animals of either sex, or on levels of endocannabinoid ligands and related N-acylethanolamines across the regions involved in the descending modulation of nociception at the time points investigated.
Mechanisms of Modulation of Ferroptosis and Its Role in Central Nervous System Diseases
Authors: Tan Qingyun , Fang Yuying , Gu Qiong
Published: June 2021

Ferroptosis is a new form of programmed cell death characterized by intracellular iron-dependent accumulation of lipid peroxide and primarily associated with iron metabolism, glutathione-dependent pathway, and coenzyme Q10-dependent pathway. Recent studies demonstrate that ferroptosis is associated with central nervous system (CNS) diseases, such as stroke, Parkinson’s disease, Alzheimer’s disease, and Huntington’s disease. This review summarizes the key regulatory mechanisms of ferroptosis and its role in CNS diseases. These updates may provide novel perspective for the development of therapeutical agents against CNS diseases.
Existing and Potential Applications of Elastography for Measuring the Viscoelasticity of Biological Tissues In Vivo
Authors: Zhang Kaiwen , Zhu Min , Thomas Evan , Hopyan Sevan , Sun Yu
Published: June 2021

Mechanical tissue properties contribute to tissue shape change during development. Emerging evidence suggests that gradients of viscoelasticity correspond to cell movement and gene expression patterns. To accurately define mechanisms of morphogenesis, a combination of precise empirical measurements and theoretical approaches are required. Here, we review elastography as a method to characterize viscoelastic properties of tissue in vivo. We discuss its current clinical applications in mature tissues and its potential for characterizing embryonic tissues.
Design and FPGA Implementation of a Pseudo-random Number Generator Based on a Hopfield Neural Network Under Electromagnetic Radiation
Authors: Yu Fei , Zhang Zinan , Shen Hui , Huang Yuanyuan , Cai Shuo , Jin Jie , Du Sichun
Published: June 2021

When implementing a pseudo-random number generator (PRNG) for neural network chaos-based systems on FPGAs, chaotic degradation caused by numerical accuracy constraints can have a dramatic impact on the performance of the PRNG. To suppress this degradation, a PRNG with a feedback controller based on a Hopfield neural network chaotic oscillator is proposed, in which a neuron is exposed to electromagnetic radiation. We choose the magnetic flux across the cell membrane of the neuron as a feedback condition of the feedback controller to disturb other neurons, thus avoiding periodicity. The proposed PRNG is modeled and simulated on Vivado 2018.3 software and implemented and synthesized by the FPGA device ZYNQ-XC7Z020 on Xilinx using Verilog HDL code. As the basic entropy source, the Hopfield neural network with one neuron exposed to electromagnetic radiation has been implemented on the FPGA using the high precision 32-bit Runge Kutta fourth-order method (RK4) algorithm from the IEEE 754-1985 floating point standard. The post-processing module consists of 32 registers and 15 XOR comparators. The binary data generated by the scheme was tested and analyzed using the NIST 800.22 statistical test suite. The results show that it has high security and randomness. Finally, an image encryption and decryption system based on PRNG is designed and implemented on FPGA. The feasibility of the system is proved by simulation and security analysis.