bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring the Common Mechanism of Fungal sRNA Transboundary Regulation of Plants Based on Ensemble Learning Methods
Authors: Chi Junxia , Zhang Hao , Zhang Tianyue , Zhao Enshuang , Zhao Tianheng , Zhao Hengyi , Yuan Shuai
Published: February 2022

Studies have found that pathogenic fungi and plants have sRNA transboundary regulation mechanisms. However, no researchers have used computer methods to carry out comprehensive studies on whether there is a more remarkable similarity in the transboundary regulation of plants by pathogenic fungi. In this direction, high-throughput non-coding sRNA data of three types of fungi and fungi-infected plants for 72 h were obtained. These include the Magnaporthe, Magnaporthe oryzae infecting Oryza sativa, Botrytis cinerea, Botrytis cinerea infecting Solanum lycopersicum, Phytophthora infestans and Phytophthora infestans infecting Solanum tuberosum. Research on these data to explore the commonness of fungal sRNA transboundary regulation of plants. First, using the big data statistical analysis method, the sRNA whose expression level increased significantly after infection was found as the key sRNA for pathogenicity, including 355 species of Magnaporthe oryzae, 399 species of Botrytis cinerea, and 426 species of Phytophthora infestans. Secondly, the target prediction was performed on the key sRNAs of the above three fungi, and 96, 197, and 112 core nodes were screened out, respectively. After functional enrichment analysis, multiple GO and KEGG_Pathway were obtained. It is found that there are multiple identical GO and KEGG_Pathway that can participate in plant gene expression regulation, metabolism, and other life processes, thereby affecting plant growth, development, reproduction, and response to the external environment. Finally, the characteristics of key pathogenic sRNAs and some non-pathogenic sRNAs are mined and extracted. Five Ensemble learning algorithms of Gradient Boosting Decision Tree, Random Forest, Adaboost, XGBoost, and Light Gradient Boosting Machine are used to construct a binary classification prediction model on the data set. The five indicators of accuracy, recall, precision, F1 score, and AUC were used to compare and analyze the models with the best parameters obtained by training, and it was found that each model performed well. Among them, XGBoost performed very well in the five models, and the AUC of the validation set was 0.86, 0.93, and 0.90. Therefore, this model has a reference value for predicting other fungi’s key sRNAs that transboundary regulation of plants.
Placental Macrophage (Hofbauer Cell) Responses to Infection During Pregnancy: A Systematic Scoping Review
Authors: Fakonti Georgia , Pantazi Paschalia , Bokun Vladimir , Holder Beth
Published: February 2022

Background

Congenital infection of the fetus via trans-placental passage of pathogens can result in severe morbidity and mortality. Even without transmission to the fetus, infection of the placenta itself is associated with pregnancy complications including pregnancy loss and preterm birth. Placental macrophages, also termed Hofbauer cells (HBCs), are fetal-origin macrophages residing in the placenta that are likely involved in responding to placental infection and protection of the developing fetus. As HBCs are the only immune cell present in the villous placenta, they represent one of the final opportunities for control of infection and prevention of passage to the developing fetus.

Objective and Rationale

The objective of this review was to provide a systematic overview of the literature regarding HBC responses during infection in pregnancy, including responses to viral, bacterial, and parasitic pathogens.

Methods

PubMed and Scopus were searched on May 20th, 2021, with no limit on publication date, to identify all papers that have studied placental macrophages/Hofbauer cells in the context of infection. The following search strategy was utilized: (hofbauer* OR “hofbauer cells” OR “hofbauer cell” OR “placental macrophage” OR “placental macrophages”) AND [infect* OR virus OR viral OR bacteri* OR parasite* OR pathogen* OR LPS OR “poly(i:c)” OR toxoplasm* OR microb* OR HIV)].

Outcomes

86 studies were identified for review. This included those that investigated HBCs in placentas from pregnancies complicated by maternal infection and in vitro studies investigating HBC responses to pathogens or Pathogen-Associated Molecular Patterns (PAMPs). HBCs can be infected by a variety of pathogens, and HBC hyperplasia was a common observation. HBCs respond to pathogen infection and PAMPs by altering their transcriptional, translational and secretion profiles. Co-culture investigations demonstrate that they can replicate and transmit pathogens to other cells. In other cases, they may eliminate the pathogen through a variety of mechanisms including phagocytosis, cytokine-mediated pathogen elimination, release of macrophage extracellular traps and HBC-antibody-mediated neutralization. HBC responses differ across gestation and may be influenced by pre-existing immunity. Clinical information, including gestational age at infection, gestational age of the samples, mode of sample collection and pregnancy outcome were missing for the majority of studies.
Feeder Cells at the Interface of Natural Killer Cell Activation, Expansion and Gene Editing
Authors: Gurney Mark , Kundu Soumyadipta , Pandey Shubham , O’Dwyer Michael
Published: February 2022

Genome engineered natural killer (NK) cell therapies are emerging as a promising cancer immunotherapy platform with potential advantages and remaining uncertainties. Feeder cells induce activation and proliferation of NK cells via cell surface receptor-ligand interactions, supported by cytokines. Feeder cell expanded NK cell products have supported several NK cell adoptive transfer clinical trials over the past decade. Genome engineered NK cell therapies, including CAR-NK cells, seek to combine innate and alloreactive NK cell anti-tumor activity with antigen specific targeting or additional modifications aimed at improving NK cell persistence, homing or effector function. The profound activating and expansion stimulus provided by feeder cells is integral to current applications of clinical-scale genome engineering approaches in donor-derived, primary NK cells. Herein we explore the complex interactions that exist between feeder cells and both viral and emerging non-viral genome editing technologies in NK cell engineering. We focus on two established clinical-grade feeder systems; Epstein-Barr virus transformed lymphoblastoid cell lines and genetically engineered K562.mbIL21.4-1BBL feeder cells.
Prevalence of Pure Red Cell Aplasia Following Major ABO-Incompatible Hematopoietic Stem Cell Transplantation
Authors: Zhu Panpan , Wu Yibo , Cui Dawei , Shi Jimin , Yu Jian , Zhao Yanmin , Lai Xiaoyu , Liu Lizhen , Xie Jue , Huang He , Luo Yi
Published: February 2022

Background

Pure red cell aplasia (PRCA) is one of the important complications in major ABO-incompatible allogeneic hematopoietic stem cell transplantation (HSCT). The established pathogenic factor of PRCA is the persistence of high anti-donor isohemagglutinins. As previously verified, the conditioning regimen and donor type were the factors associated with the development of PRCA in the small-sized studies. Currently, the prevalence, risk factors, and prognosis of PRCA are still worth studying to provide evidence.

Methods

We conducted a prospective nested case-control study to determine the prevalence, donor-related factors, and the outcomes of PRCA following major ABO-incompatible transplantation. A total of 469 patients who underwent ABO-incompatible grafts were observed.

Results

None of the patients were diagnosed with PRCA with minor or bidirectional ABO-incompatible HSCT. Thirteen of the187 patients (7%; 95% confidence interval [CI], 3.9%–11.9%) developed PRCA following major ABO-incompatible HSCT. Eleven of the 13 patients with PRCA recovered entirely. Donor type was an independent factor associated with post-HSCT PRCA (odds ratio [OR]=0.030; 95% CI, 0.003–0.321; P=0.004). The cumulative incidence rates of post-HSCT PRCA in the context of major ABO-incompatible HSCT were 0.8%, 13.1%, and 27.2% for the haploidentical donor (HID), unrelated donor, and matched related donor, respectively. No significant influence of PRCA on transplantation outcomes was observed.

In conclusion, post-HSCT PRCA is a rare and less threatening complication in major ABO-incompatible HSCT. The majority of patients with PRCA could recover. Additionally, HIDs for recipients may have a low risk of post-HSCT PRCA. This trial was registered at www.chictr.org.cn (#ChiCTR2000041412).
Lymphocyte Polarization During Immune Synapse Assembly: Centrosomal Actin Joins the Game
Authors: Cassioli Chiara , Baldari Cosima T.
Published: February 2022

Interactions among immune cells are essential for the development of adaptive immune responses. The immunological synapse (IS) provides a specialized platform for integration of signals and intercellular communication between T lymphocytes and antigen presenting cells (APCs). In the T cell the reorganization of surface molecules at the synaptic interface is initiated by T cell receptor binding to a cognate peptide-major histocompatibility complex on the APC surface and is accompanied by a polarized remodelling of the cytoskeleton and centrosome reorientation to a subsynaptic position. Although there is a general agreement on polarizing signals and mechanisms driving centrosome reorientation during IS assembly, the primary events that prepare for centrosome repositioning remain largely unexplored. It has been recently shown that in resting lymphocytes a local polymerization of filamentous actin (F-actin) at the centrosome contributes to anchoring this organelle to the nucleus. During early stages of IS formation centrosomal F-actin undergoes depletion, allowing for centrosome detachment from the nucleus and its polarization towards the synaptic membrane. We recently demonstrated that in CD4+ T cells the reduction in centrosomal F-actin relies on the activity of a centrosome-associated proteasome and implicated the ciliopathy-related Bardet-Biedl syndrome 1 protein in the dynein-dependent recruitment of the proteasome 19S regulatory subunit to the centrosome. In this short review we will feature our recent findings that collectively provide a new function for BBS proteins and the proteasome in actin dynamics, centrosome polarization and T cell activation.
Monthly Succession of Biofouling Communities and Corresponding Inter-Taxa Associations in the North- and South-West of the Arabian Gulf
Authors: Muthukrishnan Thirumahal , Hassenrück Christiane , Al Fahdi Dhikra , Jose Liny , Al Senafi Fahad , Mahmoud Huda , Abed Raeid M. M.
Published: February 2022

Marine biofouling is a complicated process involving changes within micro- and macro-fouling community, species co-occurrence, and inter-taxa association patterns. An investigation of all above-mentioned aspects has rarely been conducted so far. Our study aimed to compare the monthly succession of the biofouling community developed at two locations each in the north- (Kuwait) and south-west (Oman) of the Arabian Gulf (AG) over 6 months, and to explore the association patterns within microfouling and between micro- and macro-fouling communities on a temporal and spatial scale. Spatio-temporal effects on the abundance and composition of micro- and macro-fouling communities were detected based on total biomass, bacterial and phototroph abundances, macrofouling coverage and 16S rRNA gene sequencing. We documented the development of distinct ecological niches within the fouling community resulting in fundamentally different succession patterns depending on location. Network analysis revealed nine clusters of highly interconnected co-occurring fouling bacterial taxa (M1-M9), with strong association (both positive and negative) to microalgae and macrofoulers in both Kuwait and Oman. Early stages of Kuwait biofilm showed M7 (cyanobacterial OTUs) positively and negatively associated with the majority of diatoms and macroalgae (Cladophoraceae), respectively, unlike the later stages where M5 (composed of Vibrio spp.) was positively associated with polychaetes (Hydroides elegans). While the causal relationships behind the observed inter-taxa associations remain unknown, our study provided insights into the underlying dynamics of biofouling processes encountered in the north- and south-west of the AG. Comprehensive future investigations encompassing transcriptomic or metabolomic tools may be required to address the challenge of interpreting such complicated dynamics over time and space in a continuously changing environment.
River Runoff as a Major Driver of Anchovy (Engraulis ringens) Recruitment but Not of Common Sardine (Strangomera bentincki) in Central-South Chile
Authors: Zunguza Afonso , Montes Rodrigo M. , Cubillos Luis A. , Quiñones Renato A.
Published: February 2022

River runoff to the coastal zone is one of the most important environmental variables that influences the structure and functioning of the neritic trophic web and modulates temporal fluctuations of coastal fishery production in many ecosystems worldwide. The relationship between recruitment of anchovy (Engraulis ringens) and common sardine (Strangomera bentincki) in central-south Chile (34°–40°S) and fluctuations in river runoff was analyzed during the last two decades (1999–2018) using linear and nonlinear regression models. River runoff was also incorporated as a co-variate in Beverton-Holt (BH) stock-recruitment models. Anchovy recruitment was found to be positive and significantly associated with river runoff for all analyzed rivers both for the runoff calculated during its main reproductive period (July–October) and for each single month during this period. This detected nonlinear relationship remained significant when runoff was analyzed for the central macrozone (CMZ) and southern macrozone (SMZ). In contrast, no relationship between runoff and recruitment was detected for the common sardine in any river or macrozone (CMZ, SMZ), for each month of the main reproductive season or for the whole reproductive period (July–October). No density-dependent regulation was detected using BH stock-recruitment models for either species, with or without total freshwater input (i.e., the joint discharge of all rivers; RIVSUM index) as a covariate. Our results highlight the relevance of river runoff as a major driving factor in anchovy recruitment variability, suggesting that high (low) monthly runoff anomalies during the main reproductive period of anchovy populations markedly affect the survival of its early stages, altering recruitment success. For common sardine the runoff effect was not significant, which suggests that other oceanographic/climatic factors (wind-driven upwelling, sea surface temperature, El Niño) are more relevant in driving the variability of its recruitment than river runoff.
Does the Protection of River Basin Ecosystems Produce Broken Window Effect? Evidence From Spatial Choice Experiment in Xijiang River Basin, China
Authors: Nie Xin , Chen Zhoupeng , Yang Linfang , Qing Yiting , Wang Han
Published: February 2022

Eco-environmental protection of river basins and compensation for damages have been important issues for researchers around the world for a long time. Many studies have focused on the correlations among individual socioeconomic characteristics, ecological cognition, and differences in the willingness to pay. However, no research has been conducted from the perspective of perceived environmental quality. According to the Broken Windows Theory, the public’s willingness and behaviors regarding environmental protection are determined largely by earlier perceptions of environmental quality. Therefore, we used a spatial choice experiment to investigate the willingness of the public to pay for ecosystem restoration in the upper, middle, and lower reaches of the Xijiang River Basin in China. This paper discusses if perceived environmental quality is a factor that creates different levels in the willingness to pay. Our results show that the Broken Window Effect can better explain these differences. Living in a better ecological environment, the upper-reaches public expect to pay for the restoration of the river basin’s ecosystem to a higher state and is willing to be the “first person” to repair the “broken windows,” whereas those in the middle and lower reaches are willing to pay only for a restoration to a good state.
Theoretical and Experimental Investigation on Dynamic Response of Asphalt Pavement Under Vibration Compaction
Authors: Shan Hong-Yu , Dan Han-Cheng , Wang Shi-Ping , Liu Xiang , Wang Hao
Published: February 2022

This study aims to investigate the dynamic response regulation by combining the theoretical analysis and field test under the vibration rolling condition. Based on the viscoelastic theory of a multilayer system, the dynamic stiffness method (DSM) incorporating multidimensional Fourier transform is proposed to solve the 3-dimensional (3D) dynamic response of pavement under vibration compaction. The stiffness matrix of each pavement layer and the global stiffness matrix of the whole pavement structure are obtained. By combining vibration load with boundary conditions, the 3D exact solution is obtained and validated by the finite element method. In addition, the field test is also conducted using a series of sensors and equipment (e.g., SmartRock sensor, acceleration sensor, temperature sensors, and non-nuclear density meter) to calibrate the theoretical model to determine the wave number and dynamic modulus during the vibration rolling process. Then, considering the factors during compaction, the rules of displacement variation and pavement acceleration are investigated in terms of modulus, thickness, and density. The results show that the 3D displacement and acceleration components both vibrate with high frequencies during compaction, and peak acceleration in the vertical direction prevails. For the vertical displacement, its distribution beneath the drum of the roller is almost even except that it drops to zero abruptly around the drum edge. The relationship between thickness and acceleration follows a linear function, and the acceleration on the pavement surface rises when the thickness increases. Although the density and modulus increase with rolling times, the effect of modulus on acceleration is more obvious and prominent than that of density. In summary, the DSM presented in this article provides a robust method to calculate the dynamic response of pavement under vibratory compaction and to back-calculate the modulus of compacted pavement layers. Moreover, the regulation also sheds insight on the understanding of vibration compaction mechanism that there is a potentially strong correlation between compaction state, modulus, and vibration acceleration.
Subtypes of Premorbid Metabolic Syndrome and Associated Clinical Outcomes in Older Adults
Authors: Lin Chu-Sheng , Lee Wei-Ju , Lin Shih-Yi , Lin Hui-Ping , Chen Ran-Chou , Lin Chi-Hung , Chen Liang-Kung
Published: February 2022

Background

Metabolic syndrome has been shown to be a risk for new onset of cardiovascular disease (CVD) and type 2 diabetes. The subclasses of metabolic syndrome and any associated adverse health outcomes remain obscure. This study aimed to explore potential subtypes of metabolic syndrome, their associations with incidental diabetes, and any Major Adverse Cardiovascular Events (MACE).

Methods

Data for the retrospective cohort study were extracted from the New Taipei City Elderly Health Examination Database in the years 2014 and 2016. Demographic data, status of metabolic syndrome, its components, and latent class analysis (LCA) were analyzed. All participants were aged 65 years and older, with those having a prior history of CVD, cerebrovascular disease, diabetes mellitus (DM), and currently taking medications for hypertension, diabetes, and dyslipidemia were excluded.

Results

A total of 4,537 senior citizens were enrolled, with 2,207 (48.6%) of them identified as men. The prevalence of both metabolic syndrome and central obesity was increased with age. A 4-latent class model was fitted for participants diagnosed with metabolic syndrome. The central obesity (ABD)+ hyperglycemia (GLU)+ reduced HDL-C (HDL)+ high Blood Pressure (BP) group displayed the highest hazard ratio (HR) for predicting the new onset of diabetes, while the ABD+HDL+BP group showed a high risk for both CVD and MACE when compared after 2 years of follow-up.

Conclusions

This epidemiological analysis demonstrated that the risks of developing new-onset diabetes, CVD, and MACE varied among the different subtypes of metabolic syndrome.
Agreement of Anterior Segment Parameter Measurements With CASIA 2 and IOLMaster 700
Authors: Ruan Xiaoting , Yang GuangYao , Xia Zhaoxia , Zhang Jiaqing , Gu Xiaoxun , Tan Yuan , Liu Zhenzhen , Luo Lixia
Published: February 2022

Purpose

To compare the difference and agreement in central corneal thickness (CCT), keratometry (K), anterior chamber depth (ACD), aqueous depth (AQD), and lens thickness (LT) measured with CASIA 2 and IOLMaster 700 in patients with cataract.

Methods

A total of 81 patients with cataract (81 eyes) scheduled for phacoemulsification were prospectively collected from March to May, 2020 in the cataract department of Zhongshan Ophthalmic Center, Sun Yat-sen University, including 43 males and 38 females with age of 61.5 ± 10.6 years. CCT, anterior Kf, anterior Ks, real Kf, real Ks, ACD, AQD, and LT were measured with CASIA 2 and IOLMaster 700. Paired t-test, intraclass correlation coefficients (ICCs), 95% limit of agreement (95% LoA), and Bland-Altman plots were performed and used to analyze the difference and agreement between the two devices.

Results

There was no statistically significant difference in anterior K measurement with the CASIA 2 (44.3 ± 1.66 mm) and IOLMaster 700 (44.31 ± 1.67 mm, P = 0.483). Differences among the CCT, anterior Kf, real Kf, real Ks, ACD, AQD, and LT measured by the two instruments were statistically significant (P < 0.001). The ICCs of CCT, anterior Kf, anterior Ks, real Kf, real Ks, ACD, AQD, and LT measurements between the two devices were 0.892, 0.991, 0.991, 0.827, 0.817, 0.937, 0.926, and 0.997, respectively. The 95% LoA between CASIA 2 and IOLMaster 700 was −30.06 to 0.43 μm for CCT, −0.3 to 0.48 D for anterior Kf, −0.46 to −0.43 D for anterior Ks, −1.49 to −0.49 D for real Kf, −1.62 to −0.49 D for Real Ks, −0.03 to 0.24 mm for ACD, 0.04 to 0.25 mm for AQD, and −0.06 to 0.09 mm for LT.

Conclusion

Anterior Kf, anterior Ks, ACD, AQD, and LT have excellent agreement between the two devices. CCT, real Kf, and real Ks have moderate agreement between the two devices. It is recommended to use anterior Kf, anterior Ks, ACD, AQD, and LT interchangeably between CASIA 2 and IOLMaster 700.
Multimodal in vivo Imaging of the Integrated Postnatal Development of Brain and Skull and Its Co-modulation With Neurodevelopment in a Down Syndrome Mouse Model
Authors: Llambrich Sergi , González Rubèn , Albaigès Julia , Wouters Jens , Marain Fopke , Himmelreich Uwe , Sharpe James , Dierssen Mara , Gsell Willy , Martínez-Abadías Neus , Vande Velde Greetje
Published: February 2022

The brain and skeletal systems are intimately integrated during development through common molecular pathways. This is evidenced by genetic disorders where brain and skull dysmorphologies are associated. However, the mechanisms underlying neural and skeletal interactions are poorly understood. Using the Ts65Dn mouse model of Down syndrome (DS) as a case example, we performed the first longitudinal assessment of brain, skull and neurobehavioral development to determine alterations in the coordinated morphogenesis of brain and skull. We optimized a multimodal protocol combining in vivo micro-computed tomography (μCT) and magnetic resonance imaging (μMRI) with morphometric analyses and neurodevelopmental tests to longitudinally monitor the different systems' development trajectories during the first postnatal weeks. We also explored the impact of a perinatal treatment with green tea extracts enriched in epigallocatechin-3-gallate (GTE-EGCG), which can modulate cognition, brain and craniofacial development in DS. Our analyses quantified alterations associated with DS, with skull dysmorphologies appearing before brain anomalies, reduced integration and delayed acquisition of neurodevelopmental traits. Perinatal GTE-EGCG induced disparate effects and disrupted the magnitude of integration and covariation patterns between brain and skull. Our results exemplify how a longitudinal research approach evaluating the development of multiple systems can reveal the effect of morphological integration modulating the response of pathological phenotypes to treatment, furthering our understanding of complex genetic disorders.
Effects of Lactobacillus acidophilus KLDS1.0901 on Proliferation and Apoptosis of Colon Cancer Cells
Authors: Yue Yingxue , Wang Song , Shi Jialu , Xie Qinggang , Li Na , Guan Jiaqi , Evivie Smith Etareri , Liu Fei , Li Bailiang , Huo Guicheng
Published: February 2022

Colon cancer is the most common type of malignant tumor. The cytotoxicity effect of lactic acid bacteria may be active by inhibiting cancer cell proliferation, producing anticancer compounds, and inducing apoptosis in cancer cells, but the mechanism is unclear. Our previous study revealed that Lactobacillus acidophilus KLDS1.0901 has good probiotic properties. In this study, We screened out the highest inhibition rate of L. acidophilus KLDS1.0901 and assessed the effects on the proliferation of HT-29, Caco-2, and IEC-6 cells. Then, the apoptosis mechanism of HT-29 cells was studied when treated with L. acidophilus KLDS1.0901. Results showed that L. acidophilus KLDS1.0901 inhibited the proliferation of HT-29 and Caco-2 cells in a dose-dependent manner and reached the maximum under the condition of multiplicity of infection (MOI) = 100 (rate of Lactobacillus to cells) at 48 h. With the increase in time and MOI, reactive oxygen species in HT-29 cells, the apoptosis rates of HT-29 cells were increased, and the amount of blue fluorescence of the cells was also increased after Hoechst 33258 staining. Furthermore, L. acidophilus KLDS1.0901 reduced the mitochondrial membrane potential of HT-29 cells. Notably, 1,133 differentially expressed genes were screened by transcriptomics research, including 531 up-regulated genes and 602 down-regulated genes. These genes were involved in the nuclear factor κB and PI3K-AKT signaling pathways related to the apoptosis of HT-29 cells. These findings suggested that L. acidophilus KLDS1.0901 has the potential to be used in the development of a new type of functional foods for adjuvant treatment of colon cancer.
Cecal Microbiota of Free-Range Hens Varied With Different Rearing Enrichments and Ranging Patterns
Authors: Bari Md Saiful , Kheravii Sarbast K. , Bajagai Yadav S. , Wu Shu-Biao , Keerqin Chake , Campbell Dana L. M.
Published: February 2022

Free-range pullets are reared indoors but the adult hens can go outside which is a mismatch that may reduce adaptation in the laying environment. Rearing enrichments might enhance pullet development and adaptations to subsequent free-range housing with impact on behavior and health measures including gut microbiota. Adult free-range hens vary in range use which may also be associated with microbiota composition. A total of 1,700 Hy-Line Brown® chicks were reared indoors across 16 weeks with three enrichment treatment groups: “control” with standard litter housing, “novelty” with weekly changed novel objects, and “structural” with custom-designed perching structures in the pens. At 15 weeks, 45 pullet cecal contents were sampled before moving 1,386 pullets to the free-range housing system. At 25 weeks, range access commenced, and movements were tracked via radio-frequency identification technology. At 65 weeks, 91 hens were selected based on range use patterns (“indoor”: no ranging; “high outdoor”: daily ranging) across all rearing enrichment groups and cecal contents were collected for microbiota analysis via 16S rRNA amplicon sequencing at V3-V4 regions. The most common bacteria in pullets were unclassified Barnesiellaceae, Prevotella, Blautia and Clostridium and in hens Unclassified, Ruminococcus, unclassified Lachnospiraceae, unclassified Bacteroidales, unclassified Paraprevotellaceae YRC22, and Blautia. The microbial alpha diversity was not significant within the enrichment/ranging groups (pullets: P ≥ 0.17, hen rearing enrichment groups: P ≥ 0.06, hen ranging groups: P ≥ 0.54), but beta diversity significantly varied between these groups (pullets: P ≤ 0.002, hen rearing enrichment groups: P ≤ 0.001, hen ranging groups: P ≤ 0.008). Among the short-chain fatty acids (SCFAs), the propionic acid content was higher (P = 0.03) in the novelty group of pullets than the control group. There were no other significant differences in the SCFA contents between the rearing enrichment groups (all P ≥ 0.10), and the ranging groups (all P ≥ 0.17). Most of the genera identified were more abundant in the indoor than high outdoor hens. Overall, rearing enrichments affected the cecal microbiota diversity of both pullets and adult hens and was able to distinguish hens that remained inside compared with hens that ranging daily for several hours.
Haemonchus contortus Infection Alters Gastrointestinal Microbial Community Composition, Protein Digestion and Amino Acid Allocations in Lambs
Authors: Xiang Hai , Fang Yi , Tan Zhiliang , Zhong Rongzhen
Published: February 2022

The objective of this study was to investigate associations between gastrointestinal microbiota and protein metabolism of lambs infected with Haemonchus contortus. Sixteen male Ujumqin lambs (initial body weight = 32.4 ± 3.9 kg) were dewormed and randomly assigned to 2 equal groups, to be infected or not infected with Haemonchus contortus (GIN and CON, respectively). The experiment lasted 77 days. The GIN lambs had lower packed cell volume (PCV) and increased wormegg count (WEC) after 14 days. Furthermore, in infected lambs, there were decreases in apparent digestibility of dry matter (P = 0.011), crude protein (P = 0.004) and ether extract (P = 0.007), as well as decreased ruminal pepsin (P < 0.001) and lipase (P = 0.032) activity but increased ruminal α-amylase (P = 0.004) and cellulase activity (P = 0.002), and decreased jejunal α-amylase activity (P = 0.033). In addition, infection with H. contortus decreased alpha diversity of the gastrointestinal microbial community in the rumen, abomasum and duodenum, although microbiota associated with carbohydrate and proteolytic metabolism were increased and up to 32 KEGG pathways in the duodenum were predicted to be significantly affected. In conclusion, H. contortus infection in lambs altered the gastrointestinal microbial community composition and disturbed protein digestion and allocation of absorbed amino acids. These results provided insights into consequences of H. contortus infection in lambs and could facilitate development of novel nutritional strategies to improve animal health.
Potential of Bacillus subtilis Against SARS-CoV-2 – A Sustainable Drug Development Perspective
Authors: Khodavirdipour Amir , Chamanrokh Parastoo , Alikhani Mohammad Yousef , Alikhani Mohammad Sina
Published: February 2022

The COVID-19 pandemic had anomalous yet inevitable impacts on the world’s economies, healthcare systems, and all other aspects of life. Researchers began to uncover hidden routes to find a new horizon of hope using underrated resources. Biosurfactants are sustainable biomolecules with an active surface, unique characteristics, and extensive uses. Bacillus species showed the highest amount of biosurfactant activities and Bacillus subtilis is one of them. The antiviral, antimicrobial, and anti-inflammatory activity of B. subtilis was proven recently. The great advantage is its non-toxic nature. Pro-inflammatory cytokines including IL-1 β, 6, 8, 12, 18, and TNF-(α are secreted in higher amounts when neutrophils and monocytes are triggered by biosurfactant bacteria. This point of view furnishes the potential application of B. subtilis and its biomolecules against COVID-19, either in the form of a vaccine/therapeutic agent, for a greener environment, healthier life, and environmental sustainability. Further in vivo and clinical trials are needed to validate this hypothesis.
Rice Gall Dwarf Virus Promotes the Propagation and Transmission of Rice Stripe Mosaic Virus by Co-infected Insect Vectors
Authors: Jia Dongsheng , Luo Guozhong , Shi Wei , Liu Ye , Liu Huan , Zhang Xiaofeng , Wei Taiyun
Published: February 2022

Rice stripe mosaic virus (RSMV), a newly discovered plant cytorhabdovirus, and rice gall dwarf virus (RGDV), a plant reovirus, are transmitted by leafhopper Recilia dorsalis in a persistent-propagative manner. In this study, field surveys in Luoding city, Guangdong province of southern China, showed that RSMV and RGDV frequently co-infected rice plants. Furthermore, this co-infection had a synergistic effect on viral replication potential and pathogenicity in rice plants. Meanwhile, RSMV and RGDV also co-infected R. dorsalis vectors, and RGDV significantly promoted the propagation of RSMV in co-infected vectors. Accordingly, co-infection significantly promoted the acquisition and transmission efficiencies of RSMV by R. dorsalis. However, such co-infection did not significantly affect the propagation of RGDV in vectors. More importantly, we also observed that non-viruliferous R. dorsalis preferred to feed on co-infected rice plants, and this process further affected the feeding behavior of R. dorsalis to enhance viral release into rice phloem. These results provided the clues as to why RSMV had been a gradually expanding problem, creating an increasing risk of damage to rice production. Our findings revealed that synergism between RSMV and RGDV in their host and vector enhanced the propagation and transmission of RSMV, which will help guide the formulation of viral control strategies.
SERS Based Lateral Flow Assay for Rapid and Ultrasensitive Quantification of Dual Laryngeal Squamous Cell Carcinoma-Related miRNA Biomarkers in Human Serum Using Pd-Au Core-Shell Nanorods and Catalytic Hairpin Assembly
Authors: Li Guang , Niu Ping , Ge Shengjie , Cao Dawei , Sun Aidong
Published: February 2022

Non-invasive early diagnosis is of great significant in disease pathologic development and subsequent medical treatments, and microRNA (miRNA) detection has attracted critical attention in early cancer screening and diagnosis. However, it was still a challenge to report an accurate and sensitive method for the detection of miRNA during cancer development, especially in the presence of its analogs that produce intense background noise. Herein, we developed a surface-enhanced Raman scattering (SERS)–based lateral flow assay (LFA) biosensor, assisted with catalytic hairpin assembly (CHA) amplification strategy, for the dynamic monitoring of miR-106b and miR-196b, associated with laryngeal squamous cell carcinoma (LSCC). In the presence of target miRNAs, two hairpin DNAs could self-assemble into double-stranded DNA, exposing the biotin molecules modified on the surface of palladium (Pd)–gold (Au) core–shell nanorods (Pd-AuNRs). Then, the biotin molecules could be captured by the streptavidin (SA), which was fixed on the test lines (T1 line and T2 line) beforehand. The core–shell spatial structures and aggregation Pd-AuNRs generated abundant active “hot spots” on the T line, significantly amplifying the SERS signals. Using this strategy, the limits of detections were low to aM level, and the selectivity, reproducibility, and uniformity of the proposed SERS-LFA biosensor were satisfactory. Finally, this rapid analysis strategy was successfully applied to quantitatively detect the target miRNAs in clinical serum obtained from healthy subjects and patients with LSCC at different stages. The results were consistent with the quantitative real-time PCR (qRT-PCR). Thus, the CHA-assisted SERS-LFA biosensor would become a promising alternative tool for miRNAs detection, which showed a tremendous clinical application prospect in diagnosing LSCC.
OB-fold Families of Genome Guardians: A Universal Theme Constructed From the Small β-barrel Building Block
Authors: Bianco Piero R.
Published: February 2022

The maintenance of genome stability requires the coordinated actions of multiple proteins and protein complexes, that are collectively known as genome guardians. Within this broadly defined family is a subset of proteins that contain oligonucleotide/oligosaccharide-binding folds (OB-fold). While OB-folds are widely associated with binding to single-stranded DNA this view is no longer an accurate depiction of how these domains are utilized. Instead, the core of the OB-fold is modified and adapted to facilitate binding to a variety of DNA substrates (both single- and double-stranded), phospholipids, and proteins, as well as enabling catalytic function to a multi-subunit complex. The flexibility accompanied by distinctive oligomerization states and quaternary structures enables OB-fold genome guardians to maintain the integrity of the genome via a myriad of complex and dynamic, protein-protein; protein-DNA, and protein-lipid interactions in both prokaryotes and eukaryotes.
Programmed Cell Death and Autophagy in an in vitro Model of Spontaneous Neuroretinal Degeneration
Authors: Puertas-Neyra Kevin , Galindo-Cabello Nadia , Hernández-Rodríguez Leticia A. , González-Pérez Fernando , Rodríguez-Cabello José Carlos , González-Sarmiento Rogelio , Pastor José Carlos , Usategui-Martín Ricardo , Fernandez-Bueno Ivan
Published: February 2022

Retinal neurodegenerative diseases are the leading causes of visual impairment and irreversible blindness worldwide. Although the retinal response to injury remains closely similar between different retinal neurodegenerative diseases, available therapeutic alternatives are only palliative, too expensive, or very specific, such as gene therapy. In that sense, the development of broad-spectrum neuroprotective therapies seems to be an excellent option. In this regard, it is essential to identify molecular targets involved in retinal degeneration, such as cell death mechanisms. Apoptosis has been considered as the primary cell death mechanism during retinal degeneration; however, recent studies have demonstrated that the only use of anti-apoptotic drugs is not enough to confer good neuroprotection in terms of cell viability and preservation. For that reason, the interrelationship that exists between apoptosis and other cell death mechanisms needs to be characterized deeply to design future therapeutic options that simultaneously block the main cell death pathways. In that sense, the study aimed to characterize the programmed cell death (in terms of apoptosis and necroptosis) and autophagy response and modulation in retinal neurodegenerative diseases, using an in vitro model of spontaneous retinal neurodegeneration. For that purpose, we measured the mRNA relative expression through qPCR of a selected pool of genes involved in apoptosis (BAX, BCL2, CASP3, CASP8, and CASP9), necroptosis (MLKL, RIPK1, and RIPK3), and autophagy (ATG7, BCLIN1, LC3B, mTOR, and SQSTM1); besides, the immunoexpression of their encoding proteins (Casp3, MLKL, RIPK1, LC3B, and p62) were analyzed using immunohistochemistry. Our results showed an increase of pro-apoptotic and pro-necroptotic related genes and proteins during in vitro retinal neurodegeneration. Besides, we describe for the first time the modulation between programmed cell death mechanisms and autophagy in an in vitro retinal neurodegeneration model. This study reinforces the idea that cell death mechanisms are closely interconnected and provides new information about molecular signaling and autophagy along the retinal degeneration process.
The Updated Role of Transcranial Ultrasound Neuromodulation in Ischemic Stroke: From Clinical and Basic Research
Authors: Zhu Shuiping , Meng Bin , Jiang Jianping , Wang Xiaotao , Luo Na , Liu Ning , Shen Huaping , Wang Lu , Li Qian
Published: February 2022

Ischemic stroke is a common cause of death and disability worldwide, which leads to serious neurological and physical dysfunction and results in heavy economic and social burdens. For now, timely and effective dissolution of thrombus, and ultimately improvement in the recovery of neurological functions, is the treatment strategy focus. Recently, many studies have reported that transcranial ultrasound stimulation (TUS), as a non-invasive method, can dissolve thrombus, improve cerebral blood circulation, and exert a neuroprotective effect post-stroke. TUS can promote functional recovery and improve rehabilitation efficacy among patients with ischemic stroke. This mini-review summarizes the potential mechanism and limitation of TUS in stroke aims to provide a new strategy for the future treatment of patients with ischemic stroke.
Case Report: Management of Traumatic Carotid-Cavernous Fistulas in the Acute Setting of Penetrating Brain Injury
Authors: Loggini Andrea , Kass-Hout Tareq , Awad Issam A. , El Ammar Faten , Kramer Christopher L. , Goldenberg Fernando D. , Lazaridis Christos , Mansour Ali
Published: February 2022

Traumatic carotid-cavernous fistulas (tCCFs) after penetrating brain injury (PBI) have been uncommonly described in the literature with little guidance on optimal treatment. In this case series, we present two patients with PBI secondary to gunshot wounds to the head who acutely developed tCCFs, and we review the lead-up to diagnosis in addition to the treatment of this condition. We highlight the importance of early cerebrovascular imaging as the clinical manifestations may be limited by poor neurological status and possibly concomitant injury. Definitive treatment should be attempted as soon as possible with embolization of the fistula, flow diversion via stenting of the fistula site, and, finally, vessel sacrifice as possible therapeutic options.
Penumbra Detection With Oxygen Extraction Fraction Using Magnetic Susceptibility in Patients With Acute Ischemic Stroke
Authors: Uchida Yuto , Kan Hirohito , Inoue Hiroyasu , Oomura Masahiro , Shibata Haruto , Kano Yuya , Kuno Tomoyuki , Usami Toshihiko , Takada Koji , Yamada Kentaro , Kudo Kohsuke , Matsukawa Noriyuki
Published: February 2022

Background

The oxygen extraction fraction (OEF) has been applied to identify ischemic penumbral tissue, but is difficult to use in an urgent care setting. This study aimed to investigate whether an OEF map generated via magnetic resonance quantitative susceptibility mapping (QSM) could help identify the ischemic penumbra in patients with acute ischemic stroke.

Materials and Methods

This prospective imaging study included 21 patients with large anterior circulation vessel occlusion who were admitted <24 h after stroke onset and 21 age-matched healthy controls. We identified the ischemic penumbra as the region with a Tmax of >6 s during dynamic susceptibility contrast-magnetic resonance imaging (DSC-MRI) and calculated the perfusion-core mismatch ratio between the ischemic penumbra and infarct core volumes. The OEF values were measured based on magnetic susceptibility differences between the venous structures and brain tissues using rapid QSM acquisition. Volumes with increased OEF values were compared to the ischemic penumbra volumes using an anatomical template.

Results

Eleven patients had a perfusion-core mismatch ratio of ≥1.8, and reperfusion therapy was recommended. In these patients, the volumes with increased OEF values of >51.5%, which was defined using the anterior circulation territory OEF values from the 21 healthy controls, were positively correlated with the ischemic penumbra volumes (r = 0.636, 95% CI: 0.059 to 0.895, P = 0.035) and inversely correlated with the 30-day change in the National Institutes of Health Stroke Scale scores (r = −0.624, 95% CI: −0.891 to −0.039, P = 0.041).

Conclusion

Tissue volumes with increased OEF values could predict ischemic penumbra volumes based on DSC-MRI, highlighting the potential of the QSM-derived OEF map as a penumbra biomarker to guide treatment selection in patients with acute ischemic stroke.
Implementation of a Convolutional Neural Network for Eye Blink Artifacts Removal From the Electroencephalography Signal
Authors: Jurczak Marcin , Kołodziej Marcin , Majkowski Andrzej
Published: February 2022

Electroencephalography (EEG) signals are disrupted by technical and physiological artifacts. One of the most common artifacts is the natural activity that results from the movement of the eyes and the blinking of the subject. Eye blink artifacts (EB) spread across the entire head surface and make EEG signal analysis difficult. Methods for the elimination of electrooculography (EOG) artifacts, such as independent component analysis (ICA) and regression, are known. The aim of this article was to implement the convolutional neural network (CNN) to eliminate eye blink artifacts. To train the CNN, a method for augmenting EEG signals was proposed. The results obtained from the CNN were compared with the results of the ICA and regression methods for the generated and real EEG signals. The results obtained indicate a much better performance of the CNN in the task of removing eye-blink artifacts, in particular for the electrodes located in the central part of the head.
Identification of Molecular Signatures and Candidate Drugs in Vascular Dementia by Bioinformatics Analyses
Authors: Shu Jun , Wei Wenshi , Zhang Li
Published: February 2022

Vascular dementia (VaD) is considered to be the second most common form of dementia after Alzheimer’s disease, and no specific drugs have been approved for VaD treatment. We aimed to identify shared transcriptomic signatures between the frontal cortex and temporal cortex in VaD by bioinformatics analyses. Gene ontology and pathway enrichment analyses, protein–protein interaction (PPI) and hub gene identification, hub gene–transcription factor interaction, hub gene–microRNA interaction, and hub gene–drug interaction analyses were performed. We identified 159 overlapping differentially expressed genes (DEGs) between the frontal cortex and temporal cortex that were enriched mainly in inflammation and innate immunity, synapse pruning, regeneration, positive regulation of angiogenesis, response to nutrient levels, and positive regulation of the digestive system process. We identified 10 hub genes in the PPI network (GNG13, CD163, C1QA, TLR2, SST, C1QB, ITGB2, CCR5, CRH, and TAC1), four central regulatory transcription factors (FOXC1, CREB1, GATA2, and HINFP), and four microRNAs (miR-27a-3p, miR-146a-5p, miR-335-5p, and miR-129-2-3p). Hub gene–drug interaction analysis found four drugs (maraviroc, cenicriviroc, PF-04634817, and efalizumab) that could be potential drugs for VaD treatment. Together, our results may contribute to understanding the underlying mechanisms in VaD and provide potential targets and drugs for therapeutic intervention.
Amyloid Beta Is Internalized via Macropinocytosis, an HSPG- and Lipid Raft-Dependent and Rac1-Mediated Process
Authors: Nazere Keyoumu , Takahashi Tetsuya , Hara Naoyuki , Muguruma Kazuki , Nakamori Masahiro , Yamazaki Yu , Morino Hiroyuki , Maruyama Hirofumi
Published: February 2022

Intracellular amyloid β peptide (Aβ) accumulation has drawn attention in relation to the pathophysiology of Alzheimer’s disease in addition to its extracellular deposition as senile plaque. Cellular uptake of extracellular Aβ is one of the possible mechanisms by which intracellular Aβ deposits form. Given the relevance of Aβ inside cells, it is important to understand the mechanism by which it is taken up by them. In this study, we elucidated that Neuro2A and SH-SY5Y cells internalize specifically oligomerized Aβ in a time- and dose-dependent manner. The depletion of plasma membrane cholesterol with methyl-β-cyclodextrin or treatment with trypsin diminished the internalization of oAβ, suggesting that the oAβ uptake might be both a lipid raft-dependent and heparan sulfate proteoglycan-mediated process. Treatment with a macropinocytosis inhibitor (ethylisopropyl amiloride and wortmannin) also drastically reduced the uptake of oligomer-Aβ (oAβ). oAβ-treated cells exhibited an increase in Rac1 activity, indicating that macropinocytosis induced by oAβ is regulated by these small GTPases. These findings suggest that macropinocytosis is a major endocytic route through which oAβ42 enters cells.