bluuebunny/crossref_metadata_2025 huggingface dataset:
Comprehensive investigation into cuproptosis in the characterization of clinical features, molecular characteristics, and immune situations of clear cell renal cell carcinoma
Authors: Wang Bao , Song Qiang , Wei Yuang , Wu Xiangzheng , Han Tian , Bu Hengtao , Tang Sensheng , Qian Jian , Shao Pengfei
Published: October 2022

Background

Copper-induced cell death has been widely investigated in human diseases as a form of programmed cell death (PCD). The newly recognized mechanism underlying copper-induced cell death provided us creative insights into the copper-related toxicity in cells, and this form of PCD was termed cuproptosis.

Methods

Through consensus clustering analysis, ccRCC patients from TCGA database were classified into different subgroups with distinct cuproptosis-based molecular patterns. Analyses of clinical significance, long-term survival, and immune features were performed on subgroups accordingly. The cuproptosis-based risk signature and nomogram were constructed and validated relying on the ccRCC cohort as well. The cuproptosis scoring system was generated to better characterize ccRCC patients. Finally, in vitro validation was conducted using ccRCC clinical samples and cell lines.

Result

Patients from different subgroups displayed diverse clinicopathological features, survival outcomes, tumor microenvironment (TME) characteristics, immune-related score, and therapeutic responses. The prognostic model and cuproptosis score were well validated and proved to efficiently distinguish the high risk/score and low risk/score patients, which revealed the great predictive value. The cuproptosis score also tended out to be intimately associated with the prognosis and immune features of ccRCC patients. Additionally, the hub cuproptosis-associated gene (CAG) FDX1 presented a dysregulated expression pattern in human ccRCC samples, and it was confirmed to effectively promote the killing effects of copper ionophore elesclomol as a direct target. In vitro functional assays revealed the prominent anti-cancer role of FDX1 in ccRCC.

Conclusion

Cuproptosis played an indispensable role in the regulation of TME features, tumor progression, and long-term prognosis of ccRCC.
Immunoproteasomes control activation of innate immune signaling and microglial function
Authors: Çetin Gonca , Studencka-Turski Maja , Venz Simone , Schormann Eileen , Junker Heike , Hammer Elke , Völker Uwe , Ebstein Frédéric , Krüger Elke
Published: October 2022

Microglia are the resident immune cells of the central nervous system (CNS) and play a major role in the regulation of brain homeostasis. To maintain their cellular protein homeostasis, microglia express standard proteasomes and immunoproteasomes (IP), a proteasome isoform that preserves protein homeostasis also in non-immune cells under challenging conditions. The impact of IP on microglia function in innate immunity of the CNS is however not well described. Here, we establish that IP impairment leads to proteotoxic stress and triggers the unfolded and integrated stress responses in mouse and human microglia models. Using proteomic analysis, we demonstrate that IP deficiency in microglia results in profound alterations of the ubiquitin-modified proteome among which proteins involved in the regulation of stress and immune responses. In line with this, molecular analysis revealed chronic activation of NF-κB signaling in IP-deficient microglia without further stimulus. In addition, we show that IP impairment alters microglial function based on markers for phagocytosis and motility. At the molecular level IP impairment activates interferon signaling promoted by the activation of the cytosolic stress response protein kinase R. The presented data highlight the importance of IP function for the proteostatic potential as well as for precision proteolysis to control stress and immune signaling in microglia function.
(Not) Home alone: Antigen presenting cell – T Cell communication in barrier tissues
Authors: Neuwirth Teresa , Knapp Katja , Stary Georg
Published: October 2022

Priming of T cells by antigen presenting cells (APCs) is essential for T cell fate decisions, enabling T cells to migrate to specific tissues to exert their effector functions. Previously, these interactions were mainly explored using blood-derived cells or animal models. With great advances in single cell RNA-sequencing techniques enabling analysis of tissue-derived cells, it has become clear that subsets of APCs are responsible for priming and modulating heterogeneous T cell effector responses in different tissues. This composition of APCs and T cells in tissues is essential for maintaining homeostasis and is known to be skewed in infection and inflammation, leading to pathological T cell responses. This review highlights the commonalities and differences of T cell priming and subsequent effector function in multiple barrier tissues such as the skin, intestine and female reproductive tract. Further, we provide an overview of how this process is altered during tissue-specific infections which are known to cause chronic inflammation and how this knowledge could be harnessed to modify T cell responses in barrier tissue.
The interplay between the airway epithelium and tissue macrophages during the SARS-CoV-2 infection
Authors: Barreto-Duran Emilia , Szczepański Artur , Gałuszka-Bulaga Adrianna , Surmiak Marcin , Siedlar Maciej , Sanak Marek , Rajfur Zenon , Milewska Aleksandra , Lenart Marzena , Pyrć Krzysztof
Published: October 2022

The first line of antiviral immune response in the lungs is secured by the innate immunity. Several cell types take part in this process, but airway macrophages (AMs) are among the most relevant ones. The AMs can phagocyte infected cells and activate the immune response through antigen presentation and cytokine release. However, the precise role of macrophages in the course of SARS-CoV-2 infection is still largely unknown. In this study, we aimed to evaluate the role of AMs during the SARS-CoV-2 infection using a co-culture of fully differentiated primary human airway epithelium (HAE) and human monocyte-derived macrophages (hMDMs). Our results confirmed abortive SARS-CoV-2 infection in hMDMs, and their inability to transfer the virus to epithelial cells. However, we demonstrated a striking delay in viral replication in the HAEs when hMDMs were added apically after the epithelial infection, but not when added before the inoculation or on the basolateral side of the culture. Moreover, SARS-CoV-2 inhibition by hMDMs seems to be driven by cell-to-cell contact and not by cytokine production. Together, our results show, for the first time, that the recruitment of macrophages may play an important role during the SARS-CoV-2 infection, limiting the virus replication and its spread.
Multiple phytoplankton community responses to environmental change in a temperate coastal system: A trait-based approach
Authors: Breton Elsa , Goberville Eric , Sautour Benoit , Ouadi Anis , Skouroliakou Dimitra-Ioli , Seuront Laurent , Beaugrand Gregory , Kléparski Loïck , Crouvoisier Muriel , Pecqueur David , Salmeron Christophe , Cauvin Arnaud , Poquet Adrien , Garcia Nicole , Gohin Francis , Christaki Urania
Published: October 2022

The effect of environmental change in structuring the phytoplankton communities of the coastal waters of the Eastern English Channel was investigated by applying a trait-based approach on two decades (1996-2019) of monitoring on diatoms andPhaeocystis. We show that phytoplankton species richness in an unbalanced nutrient supply context was influenced by wind-driven processes, ecological specialization for dissolved inorganic phosphorous, temporal niche differentiation, and a competition-defense and/or a growth-defense trade-off, a coexistence mechanism where weak competitors (i.e., slower growing) are better protected against predation. Under the influence of both environmental perturbations (e.g., wind-driven processes, freshwater influence, unbalanced nutrient levels) and biotic interactions (e.g., competition, predation, facilitation), phytoplankton species exhibited specific survival strategies such as investment on growth, adaptation and tolerance of species to environmental stresses, silicification and resource specialization. These strategies have led to more speciose communities, higher productivity, functional redundancy and stability in the last decade. Our results revealed that the unbalanced nutrient reduction facilitatedPhaeocystisblooms and that anthropogenic climate warming and nitrate reduction may threaten the diatom communities of the eastern English Channel in a near future. Our results provide strong support for biogeographical historical and niche-based processes in structuring the phytoplankton community in this temperate region. The variety of species responses that we characterized in this region may help to better understand future changes in pelagic ecosystems, and can serve as a basis to consider functional approaches for future ecosystem management.
Sexual reproduction and biometry of the non-zooxanthellate papillose cup coral Paracyathus pulchellus
Authors: Marchini Chiara , Fossati Valentina , Cerpelloni Martina , Caroselli Erik , Falini Giuseppe , Dubinsky Zvy , Goffredo Stefano
Published: October 2022

Basic information on the reproductive biology of many scleractinian corals species is limited or entirely lacking, particularly from temperate zones, though it is essential for a better understanding of their ecology. This study describes the morphological aspects and the annual cycle of gametogenesis and biometric parameterss of the papillose cup coral Paracyathus pulchellus collected at Palinuro (Italy, Southern Tyrrhenian Sea), filling a knowledge gap about the reproductive biology of a widespread Mediterranean and Northern Atlantic coral. Samples of P. pulchellus were collected by SCUBA diving between 5- and 10-meters depth during 18 monthly collections from June 2010 to December 2011. Sexually active polyps displayed either oocytes or spermaries, indicating that P. pulchellus was gonochoric. The sex ratio of sexually active polyps was 1:1. Gametogenesis began with undifferentiated germ cells arose in the gastrodermis that migrated towards the mesoglea of the mesentery where they completed the development. During spermatogenesis, spermary diameter increased from 25 to 83 µm. Oocyte diameter ranged from 9 to 146 µm and during oogenesis the nucleus/cytoplasm ratio decreased due to the accumulation of yolk. The nucleus migrated to the periphery of the oocyte adhering closely to the cell membrane. No embryo was observed in the coelenteric cavity of the polyps, suggesting an external development of planktotrophic larvae due to the small-sized mature oocytes and a possible broadcast spawning reproductive mode. Gonadal index of both females and males increased significantly from August until November and fertilization took place from November to January. Only sexually inactive individuals were observed from February to April, suggesting a quiescence period in both males and females. Seasonal variations in water temperature and photoperiod may have a key role in regulating gametogenesis. The analysis of the main biometric parameters (polyp width, height, dry skeletal mass, volume, surface/volume ratio and bulk skeletal density) showed a negative correlation between size and skeletal density, and no sexual dimorphism.
Habitat type and environmental conditions influence the age and growth of a temperate marine damselfish
Authors: Williams Chelsea M. , Eagleton Jacob L. , Pondella Daniel J. , Claisse Jeremy T.
Published: October 2022

Life history parameters for fishes have generally been applied to species across their entire range, however, different ecological and environmental conditions and processes (e.g., sea surface temperature, habitat, primary productivity, fishing mortality, resource availability) influence life history patterns at smaller spatial scales. By focusing on a historically protected species, we determined how environmental and ecological factors shape patterns in growth and longevity, without the impact of fishing. The Garibaldi (Hypsypops rubicundus) is a territorial marine damselfish native to the shallow rocky reefs of southern California. Garibaldi were collected from five mainland locations and five Channel Islands throughout the Southern California Bight. Paired natural reef and artificial reef habitats (i.e., breakwaters and jetties) in each mainland location were sampled. Otolith-based ageing and biological data from these populations were used to assess how age and growth vary by location, reef type (natural/artificial), island or mainland, mean annual sea surface temperature, and/or sex. The annual formation of growth increments in otoliths was validated in-situ using tetracycline mark-recapture methods to confirm that increments are formed annually. Garibaldi grew significantly larger on artificial reefs than on natural reefs but tended to live longer on paired natural reefs. Regionally, growth and longevity followed mean annual sea surface temperature gradients, consistent with Bergmann’s rule. Garibaldi exhibited clear sexual size dimorphism; males grew larger, which is uncharacteristic for both damselfish and other marine fishes from the southern California. The Garibaldi collected for this study had a maximum age of 57 years, which makes this the longest lived damselfish species by two decades.
Exploring feedback mechanisms for nitrogen and organic carbon cycling in tropical coastal zones
Authors: Jiang Shan , Jin Laiqun , Jin Jie , Ibánhez Juan Severino Pino , Wu Ying , Zhang Jing
Published: October 2022

The anthropogenic introduction of significant amounts of reactive nitrogen in the coastal zone particularly since the discovery and application of the Haber-Bosch process has profound consequences over organic carbon storage and transformations at both regional and global scales. Here, we review our current knowledge on cause-effect chains for nitrogen, especially dissolved inorganic nitrogen, on organic carbon cycling in coastal tropical systems. We focus on the feedback mechanisms for turnover of different organic carbon species to nitrogen excess and links to current environmental and climate changes. We pay special attention to organic carbon dynamics in tropical coasts due to their high primary productivity, rapid sedimentation, and significant needs of nitrogen for agriculture and industry usages. Together with land-use changes and economy development, we highlight the vulnerability of carbon storage in tropical coasts triggered by nitrogen overloading and outline possible industrial strategies with low carbon cycling disturbance to benefit the development of tropical countries.
Mechanical, thermal, and structural investigations of chemically strengthened Na2O–CaO–Al2O3–SiO2 glasses
Authors: Karlsson Stefan , Mathew Renny , Ali Sharafat , Paemurru Mart , Anton Johan , Stevensson Baltzar , Edén Mattias
Published: October 2022

For a series of conventional soda-lime-silicate glasses with increasing Al2O3content, we investigated the thermal, mechanical, and structural properties before and after K+-for-Na+ion-exchange strengthening by exposure to molten KNO3. The Al-for-Si replacement resulted in increased glass network polymerization and lowered compactness. The glass transition temperature (Tg), hardness (H) and reduced elastic modulus (Er), of the pristine glasses enhanced monotonically for increasing Al2O3content.HandErincreased linearly up to a glass composition with roughly equal stoichiometric amounts of Na2O and Al2O3where a nonlinear dependence on Al2O3was observed, whereasHandErof the chemically strengthened (CS) glasses revealed a strictly linear dependence.Tg, on the other hand, showed linear increase with Al-for-Si for pristine glasses while for the CS glasses a linear to nonlinear trend was observed. Solid-state27Al nuclear magnetic resonance (NMR) revealed the sole presence of AlO4groups in both the pristine and CS glasses.23Na NMR and wet-chemical analysis manifested that all Al-bearing glasses had a lower and near-constant K+-for-Na+ion exchange ratio than the soda-lime-silicate glass. Differential thermal analysis of CS glasses revealed a “blurred” glass transition temperature (Tg) and an exothermic step belowTg; the latter stems from the relaxation of residual compressive stresses. The nanoindentation-derived hardness at low loads and <5 mol% Al2O3showed evidence of stress relaxation for prolonged ion exchange treatment. The crack resistance is maximized for molar ratiosn(M(2)O)/n(Al2O3)≈1for the CS glasses, which is attributed to an increased elastic energy recovery that is linked to the glass compactness.
Deep learning to infer visual acuity from optical coherence tomography in diabetic macular edema
Authors: Lin Ting-Yi , Chen Hung-Ruei , Huang Hsin-Yi , Hsiao Yu-Ier , Kao Zih-Kai , Chang Kao-Jung , Lin Tai-Chi , Yang Chang-Hao , Kao Chung-Lan , Chen Po-Yin , Huang Shih-En , Hsu Chih-Chien , Chou Yu-Bai , Jheng Ying-Chun , Chen Shih-Jen , Chiou Shih-Hwa , Hwang De-Kuang
Published: October 2022

Purpose

Diabetic macular edema (DME) is one of the leading causes of visual impairment in diabetic retinopathy (DR). Physicians rely on optical coherence tomography (OCT) and baseline visual acuity (VA) to tailor therapeutic regimen. However, best-corrected visual acuity (BCVA) from chart-based examinations may not wholly reflect DME status. Chart-based examinations are subjected findings dependent on the patient’s recognition functions and are often confounded by concurrent corneal, lens, retinal, optic nerve, or extraocular disorders. The ability to infer VA from objective optical coherence tomography (OCT) images provides the predicted VA from objective macular structures directly and a better understanding of diabetic macular health. Deviations from chart-based and artificial intelligence (AI) image-based VA will prompt physicians to assess other ocular abnormalities affecting the patients VA and whether pursuing anti-VEGF treatment will likely yield increment in VA.

Materials and methods

We enrolled a retrospective cohort of 251 DME patients from Big Data Center (BDC) of Taipei Veteran General Hospital (TVGH) from February 2011 and August 2019. A total of 3,920 OCT images, labeled as “visually impaired” or “adequate” according to baseline VA, were grouped into training (2,826), validation (779), and testing cohort (315). We applied confusion matrix and receiver operating characteristic (ROC) curve to evaluate the performance.

Results

We developed an OCT-based convolutional neuronal network (CNN) model that could classify two VA classes by the threshold of 0.50 (decimal notation) with an accuracy of 75.9%, a sensitivity of 78.9%, and an area under the ROC curve of 80.1% on the testing cohort.

Conclusion

This study demonstrated the feasibility of inferring VA from routine objective retinal images.

Translational relevance

Serves as a pilot study to encourage further use of deep learning in deriving functional outcomes and secondary surrogate endpoints for retinal diseases.
Circulating Epstein-Barr virus DNA associated with hepatic impairment and its diagnostic and prognostic role in patients with gastric cancer
Authors: He Hui-Chan , Han Rui , Xu Bo-Heng , Huang Chan , Li Min-Min , He Cai-Yun , Lin Wen-Qian
Published: October 2022

Epstein–Barr virus (EBV) infection may affect all tissues and organs of the body. Little is known about the impact of this entity on its systematic incorporation in patients with gastric cancer (GC). This study enrolled a total of 113 GC patients with EBV infection (EBVaGC) and 167 GC patients without EBV infection (EBVnGC). It was found that the CRP levels (indicative of inflammatory status) were significantly increased in EBVaGC compared with those in EBVnGC (12.11 mg/L vs. 5.72 mg/L, P = 0.008), but WBC and neutrophils counts were similar in both groups (P > 0.05). Consistent elevations in the levels of liver enzymes, ALP and GGT, with incompatible alterations in ALT or AST were observed in EBVaGC. Slightly prolonged coagulation indices, PT and INR, and decreased albumin consistently suggested impaired synthesis capability of the liver in EBVaGC (all P < 0.05). The level of circulating EBV DNA was positively correlated with the level of GGT, tumor marker CA72-4 and the lymphocyte infiltration in tumor tissues (all P < 0.05). Of note, the EBV associated high-lymphocyte infiltrated tissues presented rich CD8 + T cells. Circulating EBV DNA further showed a predictive role in distinguishing EBVaGC from EBVnGC (AUC 0.79, 95% CI 0.73 to 0.85, P < 0.001), and was associated closely with better overall survival (HR 0.45, 95% CI 0.21 to 0.96, P = 0.039). EBV infection in patients with gastric cancer may be linked to hepatic impairment and immune response. Circulating cell-free EBV DNA is not only a biomarker for the screening of an EBV-related GC subtype but is also an independently prognosis factor for the long-term survival benefit in GC patients.
International good practices on central venous catheters' placement and daily management in adults and on educational interventions addressed to healthcare professionals or awake/outpatients. Results of a scoping review compared with the existent Italian good practices
Authors: Mastrandrea Giovanni , Giuliani Rachele , Graps Elisabetta A.
Published: October 2022

This scoping review aims to check the existing international literature related to the placement and management of central venous catheters (CVCs) in adults and compare them with the Good Practices published by the Italian Society of anesthesiology intensive care (hereafter “SIAARTI Good Practices”) and the protocols written by the Italian Expert group on long-term central venous accesses (hereafter “GAVeCeLT Protocols”) and verify the existence of experiences focused on the daily assessment of the implantation site and on educational interventions on awake patients or caregivers to enhance their empowerment. A systematic search approach has been applied. Our composite research question has been primarily defined by the PICO: only patients over 18 years of age with CVC for any clinical reason except for kidney replacement therapy; placement and management of CVCs with procedures recommended by the recent international guidelines/bundles and specific educational interventions are the interventions to be compared with standard CVC placement and management without any educational interventions. In total, two different types of outcomes have been taken into consideration: catheter-related complications rate (A) and patient/caregiver involvement (B). Eligible articles have been limited to Systematic Review OR Meta-analysis OR Guidelines in Human field, focusing on adults, English language only, from January 2015 to December 2020. Searched Medical Subject Headings (MeSHs) Terms were “venous” AND “catheters,” and the correspondence with the designed PICO framework was then checked directly by the authors. A comprehensive search was conducted by two reviewers on 15 February 2021 in four databases, and 32 full-text articles were finally included and qualitatively assessed. The included articles appear to be in line with the indications provided by the available Italian Good Practices and explain the complexity of this procedure. The need to promote the use of bundles and checklists related to CVC placement and dressing procedures comes to light. These organizational technologies can be implemented following the creation of teams dedicated to venous access that are subjected to continuous training. As regards the impact of educational initiatives, implementing paths of health education and proper hospital discharge preparation for both healthcare workers and families increases safety for the patient with CVC.
Depression in non-alcoholic fatty liver disease is associated with an increased risk of complications and mortality
Authors: Ng Cheng Han , Xiao Jieling , Chew Nicholas W. S. , Chin Yip Han , Chan Kai En , Quek Jingxuan , Lim Wen Hui , Tan Darren Jun Hao , Loke Ryan Wai Keong , Tan Caitlyn , Tang Ansel Shao Pin , Goh Xin Lei , Nah Benjamin , Syn Nicholas , Young Dan Yock , Tamaki Nobuharu , Huang Daniel Q. , Siddiqui Mohammad Shadab , Noureddin Mazen , Sanyal Arun , Muthiah Mark
Published: October 2022

Background and aims

The global prevalence of non-alcoholic fatty liver disease (NAFLD) is expected to rise continuously. Furthermore, emerging evidence has also shown the potential for concomitant depression in NAFLD. This study aims to examine the prevalence, risk factors, and adverse events of depression in NAFLD and evaluate whether treated depression can reverse the increased risks of adverse outcomes.

Materials and methods

This study analyses the 2000–2018 cycles of NHANES that examined liver steatosis with fatty liver index (FLI). The relationship between NAFLD and depression was assessed with a generalized linear mix model and a sensitivity analysis was conducted in the no depression, treated depression, and untreated depression groups. Survival analysis was conducted with cox regression and fine gray sub-distribution model.

Results

A total of 21,414 patients were included and 6,726 were diagnosed with NAFLD. The risk of depression in NAFLD was 12% higher compared to non-NAFLD individuals (RR: 1.12, CI: 1.00–1.26, p = 0.04). NAFLD individuals with depression were more likely to be older, females, Hispanics or Caucasians, diabetic, and have higher BMI. Individuals with depression have high risk for cardiovascular diseases (CVD) (RR: 1.40, CI: 1.25–1.58, p < 0.01), stroke (RR: 1.71, CI: 1.27–2.23, p < 0.01), all-cause mortality (HR: 1.50, CI: 1.25–1.81, p < 0.01), and cancer-related mortality (SHR: 1.43, CI: 1.14–1.80, p = 0.002) compared to NAFLD individuals without depression. The risk of CVD, stroke, all-cause mortality, and cancer-related mortality in NAFLD individuals with treated depression and depression with untreated treatment was higher compared to individuals without depression.

Conclusion

This study shows that concomitant depression in NAFLD patients can increase the risk of adverse outcomes. Early screening of depression in high-risk individuals should be encouraged to improve the wellbeing of NAFLD patients.
Ocular biometric parameters of mild hyperopia to mild myopia children aged 6–14 years from Wenzhou optometry center: A cross-sectional study
Authors: Liu Weiqin , Liu Weishai , Wang Chenxiao
Published: October 2022

Introduction

Myopia is the most common visual disorder in school-aged children and adolescents worldwide. This study aimed to explore the ocular biometric characteristics of children aged 6–14 years from the Wenzhou optometry center and to determine the relationship between spherical equivalent refraction (SER) and macular pigment optical density (MPOD).

Subjects and methods

Participants underwent a full-scale ophthalmic examination anteriorly and posteriorly. Relevant parameters were documented, such as axial length (AL), anterior chamber depth (ACD), SER and lens thickness (LT), corneal curvature radius (CCR), and MPOD. Lens power (LP) was calculated using Bennett’s formula. Shapiro–Wilk tests and histograms were used to check the normality of the distribution of refractive and ocular biometric parameters. Scatter diagrams were adopted to analyze the relationships between refraction and parameters of ocular biometry. Multiple linear regression models were employed to fit the associated factors of AL, AL/CCR, and LP.

Results

A total of 902 mild hyperopia to mild myopia (+3.00 D ≤ SE ≤ −3.00 D) children aged 6–14 years were included. The mean age of participants was 10.03 ± 2.47 years, and the prevalence of mild hyperopia, emmetropia, and myopia was 5.65, 27.05, and 67.30%, respectively. The prevalence of mild myopia increased from 30.53% at 6 years of age to 93.62% at 14 years of age. Overall, AL, ACD, and AL/CCR increased, but LP declined from 6 to 14 years of age, whereas CCR and MPOD remained stable. An increase of 1 mm in AL was associated with −0.69 D of myopic change. A unit increase in AL/CCR was associated with −7.87 D in SER. As for the SER variance, AL explained 30.5% and AL/CCR explained 51.1%, whereas AL/CCR and LP accounted for 59.2%.

Discussion

In this work, we have studied the distributions of ocular biometric characteristics of mild hyperopia to mild myopia children from the perspective of an optometry center rather than a sampling survey. In addition, we found that children from the optometry center had a slower progression toward myopia than those from previous sampling surveys, which was an informative finding for future myopia prevention. In addition, we have made a correlation analysis between the macular pigment optical density and spherical equivalent refraction. Though, no correlation was found.
Mechanical ventilation in acute brain injury patients with acute respiratory distress syndrome
Authors: Humayun Mariyam , Premraj Lavienraj , Shah Vishank , Cho Sung-Min
Published: October 2022

Acute respiratory distress syndrome (ARDS) is commonly seen in patients with acute brain injury (ABI), with prevalence being as high as 35%. These patients often have additional risk factors for ARDS compared to general critical care patients. Lung injury in ABI occurs secondary to catecholamine surge and neuro-inflammatory processes. ARDS patients benefit from lung protective ventilation using low tidal volumes, permissive hypercapnia, high PEEP, and lower PO2 goals. These strategies can often be detrimental in ABI given the risk of brain hypoxia and elevation of intracranial pressure (ICP). While lung protective ventilation is not contraindicated in ABI, special consideration is warranted to make sure it does not interfere with neurological recovery. Permissive hypercapnia with low lung volumes can be utilized in patients without any ICP issues but those with ICP elevations can benefit from continuous ICP monitoring to personalize PCO2 goals. Hypoxia leads to poor outcomes in ABI, hence the ARDSnet protocol of lower PO2 target (55–80 mmHg) might not be the best practice in patients with concomitant ARDS and ABI. High-normal PO2 levels are reasonable in target in severe ABI with ARDS. Studies have shown that PEEP up to 12 mmHg does not cause significant elevations in ICP and is safe to use in ABI though mean arterial pressure, respiratory system compliance, and cerebral perfusion pressure should be closely monitored. Given most trials investigating therapeutics in ARDS have excluded ABI patients, focused research is needed in the field to advance the care of these patients using evidence-based medicine.
Soil nutrients and plant diversity affect ectomycorrhizal fungal community structure and functional traits across three subalpine coniferous forests
Authors: Yang Nan , Hua Jiani , Zhang Jiangbao , Liu Dong , Bhople Parag , Li Xiuxiu , Zhang Yan , Ruan Honghua , Xing Wei , Mao Lingfeng
Published: October 2022

The symbiotic relationship between ectomycorrhizal fungi (EMF) and the roots of host plants is significantly important in regulating the health and stability of ecosystems, especially of those such as the climate warming affected subalpine forest ecosystems. Therefore, from the coniferous forest systems located in the Southern Qinghai-Tibetan Plateau, root tips from three forest tree species: Pinus wallichiana, Abies spectabilis and Picea spinulosa, were collected to look for the local causes of EMF community composition and diversity patterns. The EMF colonization rate, diversity and taxonomic community structure were determined by morphotyping and sanger sequencing of the fungal ITS gene from the root tip samples. Soil exploration types were identified based on the morphologies of the ectomycorrhizas, coupled with soil properties analysis and plant diversity survey. Contrasting patterns of EMF community and functional diversity were found across the studied three forests types dominated by different coniferous tree species. In terms of associations between soil and EMF properties, the total phosphorus (TP) and nitrate (NO3−) contents in soil negatively correlated with the colonization rate and the Shannon diversity index of EMF in contrast to the positive relationship between TP and EMF richness. The soil total nitrogen (TN), ammonium (NH4+) and plant diversity together caused 57.6% of the total variations in the EMF taxonomic community structure at the three investigated forest systems. Whereas based on the soil exploration types alone, NH4+ and TN explained 74.2% of variance in the EMF community structures. Overall, the findings of this study leverage our understanding of EMF dynamics and local influencing factors in coniferous forests dominated by different tree species within the subalpine climatic zone.
Non-targeted metabonomics and transcriptomics revealed the mechanism of mulberry branch extracts promoting the growth of Sanghuangporus vaninii mycelium
Authors: Huo Jinxi , Sun Yuqing , Pan Meiliang , Ma Huanyan , Lin Tianbao , Lv Zhiqiang , Li Yougui , Zhong Shi
Published: October 2022

Sanghuangprous vaninii is a wood-inhabiting fungus, and its mycelium and fruiting body show excellent medicinal values. Mulberry is one of the major hosts of S. vaninii, however, the mechanism of mulberry affecting the growth of S. vaninii has not been reported. In the present study, a mulberry-inhabiting strain of S. vaninii was selected to explore the effects of mulberry branch extracts (MBE) on the growth of the strain. Results showed that MBE could significantly promote the growth of S. vaninii mycelium at the concentration of 0.2 g/l. After 16 days of liquid culture, the dry weight of mycelium in 0.2 g/l MBE medium was higher by three times compared with that in the control. The non-targeted metabonomic analysis of the culture medium at different culture times and concentrations was conducted to find the key components in MBE that promoted the growth of S. vaninii mycelium. Under the different concentrations of MBE culture for 10 and 16 days, 22 shared differential metabolites were identified. Next, in accordance with the peak value trend of these metabolites, HPLC–MS and liquid culture validation, four components derived from MBE (i.e., scopoletin, kynurenic acid, 3,5-dihydroxybenzoic acid and 2,4-dihydroxybenzoic acid) could significantly increase the growth rate of mycelium at the concentration of 2 mg/l. Transcriptomic and qRT-PCR analyzes showed that MBE could upregulate hydrolase-related genes, such as serine–glycine–asparaginate–histidine (SGNH) hydrolase, alpha-amylase, poly-beta-hydroxybutyrate (PHB) depolymerase, glycosyl hydrolase family 61, cerato-platanin protein and Fet3, which might enhance the nutrient absorption ability of S. vaninii. Importantly, MBE could significantly increase the content of harmine, androstenedione and vesamicol, which have been reported to possess various medicinal effects. Results suggested that MBE could be an excellent additive for liquid culture of S. vaninii mycelium, and these hydrolase-related genes also provided candidate genes for improving the nutrient absorption capacity of S. vaninii.
Phytomicrobiome communications: Novel implications for stress resistance in plants
Authors: Khanna Kanika , Kohli Sukhmeen Kaur , Sharma Nandni , Kour Jaspreet , Devi Kamini , Bhardwaj Tamanna , Dhiman Shalini , Singh Arun Dev , Sharma Neerja , Sharma Anket , Ohri Puja , Bhardwaj Renu , Ahmad Parvaiz , Alam Pravej , Albalawi Thamer H.
Published: October 2022

The agricultural sector is a foremost contributing factor in supplying food at the global scale. There are plethora of biotic as well as abiotic stressors that act as major constraints for the agricultural sector in terms of global food demand, quality, and security. Stresses affect rhizosphere and their communities, root growth, plant health, and productivity. They also alter numerous plant physiological and metabolic processes. Moreover, they impact transcriptomic and metabolomic changes, causing alteration in root exudates and affecting microbial communities. Since the evolution of hazardous pesticides and fertilizers, productivity has experienced elevation but at the cost of impeding soil fertility thereby causing environmental pollution. Therefore, it is crucial to develop sustainable and safe means for crop production. The emergence of various pieces of evidence depicting the alterations and abundance of microbes under stressed conditions proved to be beneficial and outstanding for maintaining plant legacy and stimulating their survival. Beneficial microbes offer a great potential for plant growth during stresses in an economical manner. Moreover, they promote plant growth with regulating phytohormones, nutrient acquisition, siderophore synthesis, and induce antioxidant system. Besides, acquired or induced systemic resistance also counteracts biotic stresses. The phytomicrobiome exploration is crucial to determine the growth-promoting traits, colonization, and protection of plants from adversities caused by stresses. Further, the intercommunications among rhizosphere through a direct/indirect manner facilitate growth and form complex network. The phytomicrobiome communications are essential for promoting sustainable agriculture where microbes act as ecological engineers for environment. In this review, we have reviewed our building knowledge about the role of microbes in plant defense and stress-mediated alterations within the phytomicrobiomes. We have depicted the defense biome concept that infers the design of phytomicrobiome communities and their fundamental knowledge about plant-microbe interactions for developing plant probiotics.
Lactobacillus plantarum synergistically regulates M1 macrophage polarization in resistance against Salmonella enterica serovar Typhimurium infection
Authors: Duan Bingjie , Liu Ruihan , Shi Yumeng , Sun Anqi , Tang Zhengxu , Wang Chunfeng , Hu Jingtao
Published: October 2022

Macrophage polarization affects the progression of pathogenic bacterial infections. Lactobacillus is widely used to interact with macrophages and to exert specific immunomodulatory activities. In this study, we investigated the regulation of macrophage polarization against Salmonella enterica serotype Typhimurium (STM) by Lactobacillus plantarum JL01 (LP), to explore prevention and treatment strategies for salmonellosis. We assessed the in vitro differential polarization of RAW 264.7 macrophages and mouse bone marrow macrophages (BMMs) by LP against STM, by measuring protein and cytokine levels, and bactericidal activity. In addition, we assessed the protective effects of LP against STM by evaluating weight loss, survival, the burden of STM in tissues, the polarization of macrophages in the spleen and mesenteric lymph nodes (MLNs), intestinal histopathology, and cytokine production. LP slightly affected the polarization of RAW 264.7, a slight M1-skewing. LP promoted the RAW 264.7 bactericidal activity against STM. In BMMs, M1 polarization induced by LP was significantly lower than the M1-positive phenotype. The combination of LP with M1 synergistically improved M1 polarization and bactericidal activity against STM compared to the individual effects. LP promoted the activation of the NF-κB signaling pathway. Supplementation with the NF-κB inhibitor decreased M1 polarization induced by LP. We observed the protective effect of LP against STM in C57BL/6 mice, through a decrease in weight loss, mortality, STM burden in the liver, and promotion of macrophage M1 and M2 polarization in the spleen and MLNs; though M1 was higher, it did not cause inflammatory damage. In summary, LP can synergistically promote M1 polarization in combination with the M1 phenotype through the NF-κB signaling pathway and increases resistance against S. Typhimurium infection. These findings will lay the foundation for the prevention and treatment of S. Typhimurium infections in the future.
Gut microbiome and metabolites: The potential key roles in pulmonary fibrosis
Authors: Wu Yinlan , Li Yanhong , Luo Yubin , Zhou Yu , Wen Ji , Chen Lu , Liang Xiuping , Wu Tong , Tan Chunyu , Liu Yi
Published: October 2022

There are a wide variety of microbiomes in the human body, most of which exist in the gastrointestinal tract. Microbiomes and metabolites interact with the host to influence health. Rapid progress has been made in the study of its relationship with abenteric organs, especially lung diseases, and the concept the of “gut–lung axis” has emerged. In recent years, with the in-depth study of the “gut–lung axis,” it has been found that changes of the gut microbiome and metabolites are related to fibrotic interstitial lung disease. Understanding their effects on pulmonary fibrosis is expected to provide new possibilities for the prevention, diagnosis and even treatment of pulmonary fibrosis. In this review, we focused on fibrotic interstitial lung disease, summarized the changes the gut microbiome and several metabolites of the gut microbiome in different types of pulmonary fibrosis, and discussed their contributions to the occurrence and development of pulmonary fibrosis.
Interaction of acetic acid bacteria and lactic acid bacteria in multispecies solid-state fermentation of traditional Chinese cereal vinegar
Authors: Xia Menglei , Zhang Xiaofeng , Xiao Yun , Sheng Qing , Tu Linna , Chen Fusheng , Yan Yufeng , Zheng Yu , Wang Min
Published: October 2022

The microbial community plays an important role on the solid-state fermentation (SSF) of Chinese cereal vinegar, where acetic acid bacteria (AAB) and lactic acid bacteria (LAB) are the dominant bacteria. In this study, the top-down (in situ) and bottom-up (in vitro) approaches were employed to reveal the interaction of AAB and LAB in SSF of Shanxi aged vinegar (SAV). The results of high-throughput sequencing indicates that Acetobacter pasteurianus and Lactobacillus helveticus are the predominant species of AAB and LAB, respectively, and they showed negative interrelationship during the fermentation. A. pasteurianus CGMCC 3089 and L. helveticus CGMCC 12062, both of which were isolated from fermentation of SAV, showed no nutritional competition when they were co-cultured in vitro. However, the growth and metabolism of L. helveticus CGMCC 12062 were inhibited during SSF due to the presence of A. pasteurianus CGMCC 3089, indicating an amensalism phenomenon between these two species. The transcriptomic results shows that there are 831 differentially expressed genes (|log2 (Fold Change)| > 1 and, p ≤ 0.05) in L. helveticus CGMCC 12062 under co-culture condition comparing to its mono-culture, which are mainly classified into Gene Ontology classification of molecular function, biological process, and cell composition. Of those 831 differentially expressed genes, 202 genes are up-regulated and 629 genes are down-regulated. The down-regulated genes were enriched in KEGG pathways of sugar, amino acid, purine, and pyrimidine metabolism. The transcriptomic results for A. pasteurianus CGMCC 3089 under co-culture condition reveals 529 differentially expressed genes with 393 up-regulated and 136 down-regulated, and the genes within KEGG pathways of sugar, amino acid, purine, and pyrimidine metabolism are up-regulated. Results indicate an amensalism relationship in co-culture of A. pasteurianus and L. helveticus. Therefore, this work gives a whole insight on the interaction between the predominant species in SSF of cereal vinegar from nutrient utilization, endogenous factors inhibition and the regulation of gene transcription.
Transmission pathways of campylobacter spp. at broiler farms and their environment in Brandenburg, Germany
Authors: Reichelt Benjamin , Szott Vanessa , Epping Lennard , Semmler Torsten , Merle Roswitha , Roesler Uwe , Friese Anika
Published: October 2022

Broiler meat is widely known as an important source of foodborne Campylobacter jejuni and Campylobacter coli infections in humans. In this study, we thoroughly investigated transmission pathways that may contribute to possible Campylobacter contamination inside and outside broiler houses. For this purpose we carried out a comprehensive longitudinal sampling approach, using a semi-quantitative cultivation method to identify and quantify transmissions and reservoirs of Campylobacter spp.. Three german broiler farms in Brandenburg and their surrounding areas were intensively sampled, from April 2018 until September 2020. Consecutive fattening cycles and intervening downtimes after cleaning and disinfection were systematically sampled in summer and winter. To display the potential phylogeny of barn and environmental isolates, whole genome sequencing (WGS) and bioinformatic analyses were performed. Results obtained in this study showed very high Campylobacter prevalence in 51/76 pooled feces (67.1%) and 49/76 boot swabs (64.5%). Average counts between 6.4 to 8.36 log10MPN/g were detected in pooled feces. In addition, levels of 4.7 and 4.1 log10MPN/g were detected in boot swabs and litter, respectively. Samples from the barn interior showed mean Campyloacter values in swabs from drinkers 2.6 log10MPN/g, walls 2.0 log10MPN/g, troughs 1.7 log10MPN/g, boards 1.6 log10MPN/g, ventilations 0.9 log10MPN/g and 0.7 log10MPN/g for air samples. However, Campylobacter was detected only in 7/456 (1.5%) of the environmental samples (water bodies, puddles or water-filled wheel tracks; average of 0.6 log10MPN/g). Furthermore, WGS showed recurring Campylobacter genotypes over several consecutive fattening periods, indicating that Campylobacter genotypes persist in the environment during downtime periods. However, after cleaning and disinfection of the barns, we were unable to identify potential sources in the broiler houses. Interestingly, alternating Campylobacter genotypes were observed after each fattening period, also indicating sources of contamination from the wider environment outside the farm. Therefore, the results of this study suggest that a potential risk of Campylobacter transmission may originate from present environmental sources (litter and water reservoirs). However, the sources of Campylobacter transmission may vary depending on the operation and farm environmental conditions.
Are there roles for heterogeneous ribosomes during sleep in the rodent brain?
Authors: Buchanan Isla M. , Smith Trevor M. , Gerber André P. , Seibt Julie
Published: October 2022

The regulation of mRNA translation plays an essential role in neurons, contributing to important brain functions, such as brain plasticity and memory formation. Translation is conducted by ribosomes, which at their core consist of ribosomal proteins (RPs) and ribosomal RNAs. While translation can be regulated at diverse levels through global or mRNA-specific means, recent evidence suggests that ribosomes with distinct configurations are involved in the translation of different subsets of mRNAs. However, whether and how such proclaimed ribosome heterogeneity could be connected to neuronal functions remains largely unresolved. Here, we postulate that the existence of heterologous ribosomes within neurons, especially at discrete synapses, subserve brain plasticity. This hypothesis is supported by recent studies in rodents showing that heterogeneous RP expression occurs in dendrites, the compartment of neurons where synapses are made. We further propose that sleep, which is fundamental for brain plasticity and memory formation, has a particular role in the formation of heterologous ribosomes, specialised in the translation of mRNAs specific for synaptic plasticity. This aspect of our hypothesis is supported by recent studies showing increased translation and changes in RP expression during sleep after learning. Thus, certain RPs are regulated by sleep, and could support different sleep functions, in particular brain plasticity. Future experiments investigating cell-specific heterogeneity in RPs across the sleep-wake cycle and in response to different behaviour would help address this question.