bluuebunny/crossref_metadata_2025 huggingface dataset:
Population genomic screening: Ethical considerations to guide age at implementation
Authors: Spencer Scott J. , Fullerton Stephanie M.
Published: October 2022

Currently, most genetic testing involves next generation sequencing or panel testing, indicating future population-based screening will involve simultaneous testing for multiple disease risks (called here “panel testing”). Genomic screening typically focuses on single or groups of related disorders, with little utilization of panel testing. Furthermore, the optimal age for test ordering is rarely addressed in terms of whether it should coincide with the age of majority (18 years old) or after the age of majority (26 years old). We conducted an ethical analysis utilizing a hypothetical “narrow” panel test comprised of the CDC Tier 1 Genomic Applications: Familial Hypercholesterolemia (FH), increases individuals’ cardiovascular risk due to elevated low-density lipoprotein (LDL) cholesterol levels; Hereditary Breast and Ovarian Cancer (HBOC), increases lifetime risk of developing cancer; and Lynch Syndrome (LS), increases lifetime risk of developing colorectal cancer. We conducted a utilitarian analysis, on the assumption that health systems seek to maximize utility for patients. Screening at the “age of majority” is preferred for FH due to lowering FH patients’ cholesterol levels via statins providing high lifetime benefits and low risks. Screening “after the age of majority” is preferred for HBOC and LS due to availability of effective surveillance, the recommendation for screening activities to begin at age 26, and prophylactic interventions connected to surveillance. We also utilized a supplemental principlist-based approach that identified relevant concerns and trade-offs. Consideration of clinical, non-clinical, and family planning implications suggests narrow panel testing would be best deployed after 26 (rather than at 18) years of age.
Progress in research on the role of exosomal miRNAs in the diagnosis and treatment of cardiovascular diseases
Authors: Xu Jinyu , Wang Weitie , Wang Yong , Zhu Zhicheng , Li Dan , Wang Tiance , Liu Kexiang
Published: October 2022

Cardiovascular diseases are the most common diseases threatening the health of the elderly, and the incidence and mortality rates associated with cardiovascular diseases remain high and are increasing gradually. Studies on the treatment and prevention of cardiovascular diseases are underway. Currently, several research groups are studying the role of exosomes and biomolecules incorporated by exosomes in the prevention, diagnosis, and treatment of clinical diseases, including cardiovascular diseases. Now, based on the results of published studies, this review discusses the characteristics, separation, extraction, and identification of exosomes, specifically the role of exosomal miRNAs in atherosclerosis, myocardial injury and infarction, heart failure, aortic dissection, myocardial fibrosis, ischemic reperfusion, atrial fibrillation, and other diseases. We believe that the observations noted in this article will aid in the prevention, diagnosis, and treatment of cardiovascular diseases.
The therapeutic effect and mechanism of melatonin on osteoarthritis: From the perspective of non-coding RNAs
Authors: Li Shuai , Si Haibo , Xu Jiawen , Liu Yuan , Shen Bin
Published: October 2022

Osteoarthritis (OA) is a slowly progressing and irreversible joint disease. The existing non-surgical treatment can only delay its progress, making the early treatment of OA a research hotspot in recent years. Melatonin, a neurohormone mainly secreted by the pineal gland, has a variety of regulatory functions in different organs, and numerous studies have confirmed its therapeutic effect on OA. Non-coding RNAs (ncRNAs) constitute the majority of the human transcribed genome. Various ncRNAs show significant differentially expressed between healthy people and OA patients. ncRNAs play diverse roles in many cellular processes and have been implicated in many pathological conditions, especially OA. Interestingly, the latest research found a close interaction between ncRNAs and melatonin in regulating the pathogenesis of OA. This review discusses the current understanding of the melatonin-mediated modulation of ncRNAs in the early stage of OA. We also delineate the potential link between rhythm genes and ncRNAs in chondrocytes. This review will serve as a solid foundation to formulate ideas for future mechanistic studies on the therapeutic potential of melatonin and ncRNAs in OA and better explore the emerging functions of the ncRNAs.
Identification and verification of IGFBP3 and YTHDC1 as biomarkers associated with immune infiltration and mitophagy in hypertrophic cardiomyopathy
Authors: Li Yao , Zhang Wei , Dai Yan , Chen Keping
Published: October 2022

Background: Hypertrophic cardiomyopathy (HCM) is the main cause of sudden cardiac death among young adults, yet its pathogenesis remains vague. N6-methyladenosine (m6A) methylation modification was involved in various cardiovascular diseases such as coronary heart disease and heart failure, although its influence on HCM remains unclear. This study aimed to explore the potential role of m6A in the diagnosis and pathogenesis of HCM.

Methods: GSE36961 including 106 HCM and 39 controls was used in the study. The HCM-related m6A regulators were selected using support vector machine recursive feature elimination and random forest algorithm. A significant gene signature was then established using least absolute shrinkage and selection operator and then verified by GSE130036. Subgroup classification of HCM was performed based on the expression of m6A biomarkers. Gene set variation analysis was employed to explore the functional difference between distinct subgroups. Weighted gene co-expression network analysis was used to determine the m6A-related hub module. Single-sample gene set enrichment analysis was conducted to assess the immune and mitophagy features between subgroups. Besides, transfection of recombinant plasmids with targeted genes into H9c2 cells was performed to further verify the function of the significant biomarkers.

Results: Significant difference existed in m6A landscape between HCM and control patients, among which IGFBP3 and YTHDC1 were identified as the independent biomarkers of HCM. Highly infiltrated immune cells (MDSC, macrophages, etc.), more enriched immune-related pathways (TNFα signaling via NFκB and IL6-JAK-STAT3 signaling) and cardiac remodeling-associated pathways (epithelial mesenchymal transition, angiogenesis, etc.) were identified in the subgroup with higher IGFBP3. Consistently, overexpression of IGFBP3 in H9c2 cells led to upregulation of extracellular-matrix-related genes (COL1A2, COL3A1 and MMP9) and inflammation-related genes (TNFα and IL6). Besides, higher YTHDC1 expression seemed to be consistent with less-activated mitophagy (PINK1-PRKN mediated mitophagy) and energy metabolism. Further experiments demonstrated that overexpression of YTHDC1 resulted in up-regulation of PINK and PRKN in cardiomyocytes, which are essential genes mediating mitophagy.

Conclusion: Two m6A readers (IGFBP3 and YTHDC1) well distinguished HCM and may facilitate clinical diagnosis. IGFBP3 may play a role in the immune-microenvironments and remodeling of cardiac tissues, while YTHDC1 may influence mitophagy and energy metabolism in HCM.
MiR-585-5p impedes gastric cancer proliferation and metastasis by orchestrating the interactions among CREB1, MAPK1 and MITF
Authors: Wang Yunwei , Li Ming , Zeng Jiaoxia , Yang Yunshu , Li Zengshan , Hu Sijun , Yang Fangfang , Wang Na , Wang Wenlan , Tie Jun
Published: October 2022

Background

Gastric cancer (GC) is one of the most malignant and lethal cancers worldwide. Multiple microRNAs (miRNAs) have been identified as key regulators in the progression of GC. However, the underlying pathogenesis that miRNAs govern GC malignancy remains uncertain. Here, we identified a novel miR-585-5p as a key regulator in GC development.

Methods

The expression of miR-585-5p in the context of GC tissue was detected by in situ hybridization for GC tissue microarray and assessed by H-scoring. The gain- and loss-of-function analyses comprised of Cell Counting Kit-8 assay and Transwell invasion and migration assay. The expression of downstream microphthalmia-associated transcription factor (MITF), cyclic AMP-responsive element-binding protein 1 (CREB1) and mitogen-activated protein kinase 1 (MAPK1) were examined by Immunohistochemistry, quantitative real-time PCR and western blot. The direct regulation between miR-585-5p and MITF/CREB1/MAPK1 were predicted by bioinformatic analysis and screened by luciferase reporter assay. The direct transcriptional activation of CREB1 on MITF was verified by luciferase reporter assay, chromatin immunoprecipitation (ChIP) and electrophoretic mobility shift assays (EMSAs). The interaction between MAPK1 and MITF was confirmed by co-immunoprecipitation (Co-IP) and immunofluorescent double-labelled staining.

Results

MiR-585-5p is progressively downregulated in GC tissues and low miR-585-5p levels were strongly associated with poor clinical outcomes. Further gain- and loss-of-function analyses showed that miR-585-5p possesses strong anti-proliferative and anti-metastatic capacities in GC. Follow-up studies indicated that miR-585-5p targets the downstream molecules CREB1 and MAPK1 to regulate the transcriptional and post-translational regulation of MITF, respectively, thus controlling its expression and cancer-promoting activity. MiR-585-5p directly and negatively regulates MITF together with CREB1 and MAPK1. According to bioinformatic analysis, promotor reporter gene assays, ChIP and EMSAs, CREB1 binds to the promotor region to enhance transcriptional expression of MITF. Co-IP and immunofluorescent double-labelled staining confirmed interaction between MAPK1 and MITF. Protein immunoprecipitation revealed that MAPK1 enhances MITF activity via phosphorylation (Ser73). MiR-585-5p can not only inhibit MITF expression directly, but also hinder MITF expression and pro-cancerous activity in a CREB1-/MAPK1-dependent manner indirectly.

Conclusions

In conclusion, this study uncovered miR-585-5p impedes gastric cancer proliferation and metastasis by orchestrating the interactions among CREB1, MAPK1 and MITF.
Neglected, yet significant role of FOXP1 in T-cell quiescence, differentiation and exhaustion
Authors: Kaminskiy Yaroslav , Kuznetsova Varvara , Kudriaeva Anna , Zmievskaya Ekaterina , Bulatov Emil
Published: October 2022

FOXP1 is ubiquitously expressed in the human body and is implicated in both physiological and pathological processes including cancer. However, despite its importance the role of FOXP1 in T-cells has not been extensively studied. Although relatively few phenotypic and mechanistic details are available, FOXP1 role in T-cell quiescence and differentiation of CD4+ subsets has recently been established. FOXP1 prevents spontaneous T-cell activation, preserves memory potential, and regulates the development of follicular helper and regulatory T-cells. Moreover, there is growing evidence that FOXP1 also regulates T-cell exhaustion. Altogether this makes FOXP1 a crucial and highly undervalued regulator of T-cell homeostasis. In this review, we discuss the biology of FOXP1 with a focus on discoveries made in T-cells in recent years.
Porpoises after dark: Seasonal and diel patterns in Pacific harbour porpoise (Phocoena phocoena vomerina) aggregations at one of North America’s fastest growing ports
Authors: Dracott Karina , Robinson Chloe V. , Brown-Dussault Alice , Birdsall Caitlin , Barrett-Lennard Lance
Published: October 2022

Pacific Harbour Porpoise (Phocoena phocoena vomerina) occupy a large range throughout coastal waters of British Columbia. Despite their wide distribution, they remain largely data-deficient regarding abundance and population trends, and as such are listed as Special Concern under the Species At Risk Act. Harbour porpoises are also particularly sensitive to disturbance, especially vessel-related acoustic disturbance. Large aggregations of harbour porpoise have been documented in waters around the entrance to the Port of Prince Rupert during the winter months, however little is known about the annual fine-scale activity of this species in this highly trafficked area. In this multi-year study, we used a combination of land-based visual surveys and passive acoustic monitoring (PAM) devices (C-PODs and F-PODs) to address data gaps regarding density, diel patterns, and seasonality of harbour porpoise around Prince Rupert. Echolocation activity was detected during 96% of the 1086 C-POD deployment days and 100% of the 727 F-POD deployment days, with 86% of visual surveys recording harbour porpoise presence. We detected strong seasonal and diel trends in activity, with echolocation peaks between April and June and during the hours of darkness throughout the year. There was a notable increase in daytime activity of harbour porpoise between January and March, which coincides with the months of large aggregation observations. This study indicates that despite the constant presence of large vessels, harbour porpoise continue to persist within waters surrounding Prince Rupert. This suggests the area is an important habitat for this species and also may indicate some extent of acclimatization to localized disturbance.
Dynamic design and analysis of subsea CO2 discharging flowline for cargo submarines used for CCS in low-carbon and renewable energy value chains
Authors: Dai Tianjiao , Yang Shuo , Xing Yihan , Ma Yucong
Published: October 2022

Developing offshore low carbon and renewable energy value chains to realize a net-zero energy future requires combining offshore renewable energy and carbon capture storage (CCS) solutions. The subsea shuttle tanker (SST) was presented in recently published works to accelerate the adoption of offshore CCS systems. The SST is a novel underwater vessel designed to transport CO2 autonomously from offshore facilities to subsea wells for direct injection at marginal fields using a flowline connected. The SST will be subjected to stochastic currents and experience dynamic responses during this offloading process. The offloading flowline must be designed to handle this dynamic response. As such, this paper establishes the baseline design for this flowline. The cross-section and global configuration designs drive the flowline design. For the cross-section design, the pressure containment, collapse and local buckling criteria defined in DNV-OS-F101 are applied to validate the required structural capacity at specified water depths. For the configuration design, the principle factors concerning the water depth, internal flow rate, and current speed are investigated to further validate the stress capacity according to the allowed von Mises stress level for a more robust baseline design. Finally, the flowline connecting and disassembly methodology is proposed, and the critical factor of well-coordinated speed between flowline and SST is investigated to avoid overbending during the lifting and lowering phases.
Amino acid δ13C and δ15N fingerprinting of sea ice and pelagic algae in Canadian Arctic and Subarctic Seas
Authors: Chen Shao-Min , Mudie Peta , Sherwood Owen A.
Published: October 2022

The on-going decline in Arctic sea ice represents a significant loss of habitat for sea ice algae, which are a major contributor to primary production in the Arctic. Data on sea ice algal production is limited due to difficulties in both accessing sea-ice and sampling under-ice algae. Compound-specific isotope analysis (CSIA) of amino acids (AAs) is emerging as a powerful tool to trace element origins and biogeochemical processes in marine food webs and may address the knowledge gaps in sea ice algal productivity dynamics. Here we measured δ13C-AA and δ15N-AA in natural communities of sea ice and pelagic algae collected from regions offshore Labrador and Nunavut, Canada. Significant difference in δ13C-AA patterns between sea ice and pelagic algae was observed in different size classes. This difference was further supported by multivariate analyses based on normalized δ13C of essential amino acids (EAAs), which demonstrated a clear separation between sea ice and pelagic algae. Beta (β) values and trophic position (TP) calculated from δ15N of Glutamic Acid and Phenylalanine (Phe) and ∑V parameter for microbial resynthesis indicated a slightly higher heterotrophic biomass in pelagic and sea ice samples as compared to cultured samples. This finding is consistent with the Phe-normalized δ15N of Alanine and Threonine, which provided better separations between sea ice/pelagic algae and other end-member groups. Overall, our study provides first insights into the potential differences in δ13C-AA and δ15N-AA patterns between sea ice and pelagic algae and suggests carbon of sea ice origins may be distinguished from pelagic sources using CSIA-AA approach. These observations highlight the potential of CSIA-AA to estimate proportional contributions of sea ice and pelagic algae to export production and efficiency of benthic-pelagic coupling in polar marine environments.
Investigating hardware acceleration for simulation of CFD quantum circuits
Authors: Moawad Youssef , Vanderbauwhede Wim , Steijl René
Published: October 2022

Among the many computational models for quantum computing, the Quantum Circuit Model is the most well-known and used model for interacting with current quantum hardware. The practical implementation of quantum computers is a very active research field. Despite this progress, access to physical quantum computers remains relatively limited. Furthermore, the existing machines are susceptible to random errors due to quantum decoherence, as well as being limited in number of qubits, connectivity and built-in error correction. Simulation on classical hardware is therefore essential to allow quantum algorithm researchers to test and validate new algorithms in a simulated-error environment. Computing systems are becoming increasingly heterogeneous, using a variety of hardware accelerators to speed up computational tasks. One such type of accelerators, Field Programmable Gate Arrays (FPGAs), are reconfigurable circuits that can be programmed using standardized high-level programming models such as OpenCL and SYCL. FPGAs allow to create specialized highly-parallel circuits capable of mimicking the quantum parallelism properties of quantum gates, in particular for the class of quantum algorithms where many different computations can be performed concurrently or as part of a deep pipeline. They also benefit from very high internal memory bandwidth. This paper focuses on the analysis of quantum algorithms for applications in computational fluid dynamics. In this work we introduce novel quantum-circuit implementations of model lattice-based formulations for fluid dynamics, specifically the D1Q3 model using quantum computational basis encoding, as well as, efficient simulation of the circuits using FPGAs. This work forms a step toward quantum circuit formulation of the Lattice Boltzmann Method (LBM). For the quantum circuits implementing the nonlinear equilibrium distribution function in the D1Q3 lattice model, it is shown how circuit transformations can be introduced that facilitate the efficient simulation of the circuits on FPGAs, exploiting their fine-grained parallelism. We show that these transformations allow us to exploit more parallelism on the FPGA and improve memory locality. Preliminary results show that for this class of circuits the introduced transformations improve circuit execution time. We show that FPGA simulation of the reduced circuits results in more than 3× improvement in performance per Watt compared to the CPU simulation. We also present results from evaluating the same kernels on a GPU.
Role of N-acetylcysteine treatment in women with advanced age undergoing IVF/ICSI cycles: A prospective study
Authors: Li Xiufang , Wang Zhongqing , Wang Huidan , Xu Haiyan , Sheng Yan , Lian Fang
Published: October 2022

Objective

The main objective of this study was to explore the efficacy of a new antioxidant N-acetylcysteine (NAC) supplementation in reproductive outcomes of advanced age women undergoing in vitro fertilization/intracytoplasmic sperm injection-embryo transfer (IVF/ICSI-ET), and the effect on the expression of L-glutathione (GSH) in follicular fluid (FF) and mitochondrial DNA (mtDNA) copy number of granulosa cells.

Methods

The present prospective randomized controlled study was conducted in 200 patients with advanced age women undergoing GnRH antagonist protocol. The treatment group (group A) consisted of 100 women who received N-acetylcysteine treatment from the menstrual phase of the previous cycle for about 45 days using the GnRH antagonist protocol. The control group (group B) consisted of 100 women who received the same protocol without N-acetylcysteine. Total gonadotrophin dosage the number of oocyte received, high-quality blastocysts, and pregnancy outcomes were compared between two groups. Pregnancy outcomes included biochemical pregnancy rate, clinical pregnancy rate, embryo implantation rate, ectopic pregnancy rate, multiple pregnancy rate, and ongoing pregnancy rate. Follicular fluid (FF) was collected after oocytes were gathered. The GSH content in the FF was tested with enzyme linked immunosorbent assay (ELISA). The mtDNA copy number of the granulosa cells was measured using real-time PCR techniques.

Results

Total doses of Gn in the NAC treatment group were less than those in the control group (2385.50 ± 879.19 vs. 2527.63 ± 1170.33, P = 0.047). Compared with the control, the number of high-quality blastocysts in NAC treatment increased significantly (1.82 ± 2.12 vs. 1.43 ± 1.58, p = 0.014). Clinical pregnancy rates did not differ in both groups (all P > 0.05). At the same time, the GSH content in the FF differed significantly between the two groups (1.88 ± 1.23 vs. 1.07 ± 0.70, p = 0.001). There was no significant difference in the mtDNA copy number between the two groups (P = 0.157).

Conclusion

A combination of NAC and Gn treatment is capable of improving the ovarian response to superovulation drugs in assisted reproductive technologies (ARTs) and also in aged populations. The addition of NAC during IVF can improve the quality of blastocysts in advanced age female subjects. However, more clinical trials are required to be designed to confirm this conclusion in future.

Ethics and dissemination

The experiment solicited approval from the Institutional ethics committee of the Affiliated Reproductive Hospital of Shandong University. All the participants provided written informed consent. This survey was conducted as per the Declaration of Helsinki and relevant amendments.

Trial registration number

www.chictr.org.cn, identifier ChiCTR2100048297.
The effectiveness and safety of the rapid titration strategy of background controlled-release oxycodone hydrochloride for patients with moderate-to-severe cancer pain: A retrospective cohort study
Authors: Feng Weineng , Wang Yufeng , Ran Fengming , Mao Yong , Zhang Helong , Wang Qifeng , Lin Wen , Wang Zhidong , Hu Jianli , Liao Wangjun , Zhang Tao , Chu Qian , Xiong Weijie , Yi Tienan , Yi Jiqun , Ma Shoucheng , Sun Yi , Meng Lingzhan , Liu Chunling , Zhou Silang , Zheng Dengyun , Wang Shubin , Lin Haifeng , Fang Wenzheng , Li Jun , Wu Minhui
Published: October 2022

Background

Oxycodone hydrochloride is a semisynthetic narcotic analgesic agent. This study aimed to explore optimal titration strategy of controlled-release (CR) oxycodone hydrochloride in patients with cancer pain.

Methods

258 patients, who used regular strong opioids (morphine and CR oxycodone hydrochloride) for cancer pain across 25 three grade class hospitals in China during January 15th 2017 to April 30th 2017, were retrospectively studied. The patients were divided into 4 groups according to treatment regimens titrated. The pain remission rate and numeric rating scale (NRS) of cancer pain was recorded at 0, 12, 24, 36, 48, 60, 72 h after opioid titration. The incidence of adverse events (AEs) with therapy were also observed.

Results

12 h after treatment, pain remission rate of Group B, C and D was significantly higher (P < 0.001) than Group A. For the complete remission rate, there were also significant differences among the four groups (P < 0.001). No significant difference was found among four groups for pain remission rate at 24, 72 h after treatment. Multiple comparison of NRS scores showed that the both Group B and C varied significantly with Group D (P = 0.028, P = 0.05, respectively), showing superior analgesic effect over Group D. AEs were significantly different among groups (P < 0.01), with the most frequent AEs in Group A, lowest in Group B.

Conclusion

The rapid titration strategy of background CR oxycodone hydrochloride was effectiveness and safety in patients with moderate-to-severe cancer pain.
Comparative transcriptomics reveal different genetic adaptations of biofilm formation in Bacillus subtilis isolate 1JN2 in response to Cd2+ treatment
Authors: Yang Wei , Yan Haixia , Dong Guanghui , Li Zhengpeng , Jiang Chunhao , Gu Dalu , Niu Dongdong , Zhou Danni , Luo Yuming
Published: October 2022

Biofilm plays important roles in the life cycle of Bacillus species, such as promoting host and object surface colonization and resisting heavy metal stress. This study utilized transcriptomics to evaluate the impacts of cadmium on the components, morphology, and function of biofilms of Bacillus subtilis strain 1JN2. Under cadmium ion stress, the morphology of the B. subtilis 1JN2 biofilm was flattened, and its mobility increased. Moreover, differential gene expression analysis showed that the main regulator of biofilm formation, Spo0A, decreased in expression under cadmium ion stress, thereby inhibiting extracellular polysaccharide synthesis through the SinI/SinR two-component regulatory system and the AbrB pathway. Cadmium ion treatment also increased the SigD content significantly, thereby increasing the expression of the flagella encoding and assembly genes in the strain. This promoted poly-γ-glutamic acid production via the DegS/DegU two-component regulatory system and the conversion of biofilm extracellular polysaccharide to poly-γ-glutamic acid. This conferred cadmium stress tolerance in the strain. Additionally, the cadmium ion-mediated changes in the biofilm composition affected the colonization of the strain on the host plant root surface. Cadmium ions also induced surfactin synthesis. These findings illustrate the potential of Bacillus species as biocontrol strains that can mitigate plant pathogenic infections and heavy metal stress. The results also provide a basis for the screening of multifunctional biocontrol strains.
Bacillus H47 triggers Olea europaea metabolism activating DOXP and shikimate pathways simultaneously and modifying leaf extracts’ antihypertensive activity
Authors: Galicia-Campos Estrella , García-Villaraco Ana , Montero-Palmero M. B. , Gutiérrez-Mañero F. Javier , Ramos-Solano Beatriz
Published: October 2022

Improvement of plant adaptation by beneficial bacteria (PGPB) may be achieved by triggering multiple pathways to overcome the environmental stress on plant’s growth cycle, activating plant’s metabolism. The present work reports the differential ability of three Bacillus strains to trigger olive tree metabolism, among which, only H47 was outstanding increasing iridoid and flavonol concentration. One-year old olive seedlings grown open air, under harsh conditions of water shortage in saline soils, were root-inoculated with three Bacillus PGPB strains throughout a 12-month period after which, photosynthesis was determined; photosynthetic pigments and bioactive secondary metabolites (iridoids and flavonols) were analyzed, and a study of gene expression of both pathways involved was undertaken to unravel molecular targets involved in the activation. All three strains increased plant fitness based on photosynthetic values, increasing energy dissipation capacity to lower oxidative stress; only H47 increased CO2 fixation and transpiration. Bacillus H47 was found to trigger synthases in the DOXP pathway (up to 5-fold in DOXP-synthase, 3.5-fold in Iridoid synthase, and 2-fold in secologanin synthase) associated to a concomitant increase in iridoids (up to 5-fold in oleuropein and 2-fold in its precursor secologanin). However, despite the 2-fold increases detected in the two predominant flavonols, gene expression was not enhanced, suggesting involvement of a pulse activation model proposed for innate immunity. Furthermore, the activity of leaf extracts to inhibit Angiotensin Converting Enzyme was evaluated, to explore further uses of plant debris with higher added value. Despite the increases in iridoids, leaf extracts from H47 did not increase ACE inhibition, and still, increased antihypertensive potential in oil obtained with this strain is to be explored, as leaves are the source for these metabolites which further translocate to fruits. In summary, Bacillus H47 is an effective strain to increase plant adaptation to dry and saline environments, activates photosynthesis and secondary metabolism in olive tree.
Effective data filtering is prerequisite for robust microbial association network construction
Authors: Wang Mengqi , Tu Qichao
Published: October 2022

Microorganisms do not exist as individual population in the environment. Rather, they form complex assemblages that perform essential ecosystem functions and maintain ecosystem stability. Besides the diversity and composition of microbial communities, deciphering their potential interactions in the form of association networks has attracted many microbiologists and ecologists. Much effort has been made toward the methodological development for constructing microbial association networks. However, microbial profiles suffer dramatically from zero values, which hamper accurate association network construction. In this study, we investigated the effects of zero-value issues associated with microbial association network construction. Using the TARA Oceans microbial profile as an example, different zero-value-treatment approaches were comparatively investigated using different correlation methods. The results suggested dramatic variations of correlation coefficient values for differently treated microbial profiles. Most specifically, correlation coefficients among less frequent microbial taxa were more affected, whichever method was used. Negative correlation coefficients were more problematic and sensitive to network construction, as many of them were inferred from low-overlapped microbial taxa. Consequently, microbial association networks were greatly differed. Among various approaches, we recommend sequential calculation of correlation coefficients for microbial taxa pairs by excluding paired zero values. Filling missing values with pseudo-values is not recommended. As microbial association network analyses have become a widely used technique in the field of microbial ecology and environmental science, we urge cautions be made to critically consider the zero-value issues in microbial data.
Multigene phylogeny, phylogenetic network, and morphological characterizations reveal four new arthropod-associated Simplicillium species and their evolutional relationship
Authors: Chen Wanhao , Liang Jiandong , Ren Xiuxiu , Zhao Jiehong , Han Yanfeng , Liang Zongqi
Published: October 2022

Simplicillium species are widely distributed and commonly found on various substrates. A minority of species are associated with arthropods. A spider-associated species Simplicillium araneae, and three insect-associated species, Simplicillium coleopterorum, Simplicillium guizhouense, and Simplicillium larvatum, are proposed as novel species based on a multi-locus phylogenetic analysis and morphological characteristics. These Simplicillium species completely fit the nutritional model of Hypocreales fungi and could be used as a model to study their evolutionary relationship. A phylogenetic network analysis based on ITS sequences suggests that a host jump was common among Simplicillium species, and S. araneae may have originally come from an insect host and then jumped to a spider host. However, the evolutionary relationship of S. coleopterorum, S. guizhouense, and S. larvatum was not clear in the phylogenetic network and more sequencing information should be added to the network. In addition, strain CBS 101267 was identified as Simplicillium subtropicum.
Inference of pan-cancer related genes by orthologs matching based on enhanced LSTM model
Authors: Wang Chao , Zhang Houwang , Ma Haishu , Wang Yawen , Cai Ke , Guo Tingrui , Yang Yuanhang , Li Zhen , Zhu Yuan
Published: October 2022

Many disease-related genes have been found to be associated with cancer diagnosis, which is useful for understanding the pathophysiology of cancer, generating targeted drugs, and developing new diagnostic and treatment techniques. With the development of the pan-cancer project and the ongoing expansion of sequencing technology, many scientists are focusing on mining common genes from The Cancer Genome Atlas (TCGA) across various cancer types. In this study, we attempted to infer pan-cancer associated genes by examining the microbial model organism Saccharomyces Cerevisiae (Yeast) by homology matching, which was motivated by the benefits of reverse genetics. First, a background network of protein-protein interactions and a pathogenic gene set involving several cancer types in humans and yeast were created. The homology between the human gene and yeast gene was then discovered by homology matching, and its interaction sub-network was obtained. This was undertaken following the principle that the homologous genes of the common ancestor may have similarities in expression. Then, using bidirectional long short-term memory (BiLSTM) in combination with adaptive integration of heterogeneous information, we further explored the topological characteristics of the yeast protein interaction network and presented a node representation score to evaluate the node ability in graphs. Finally, homologous mapping for human genes matched the important genes identified by ensemble classifiers for yeast, which may be thought of as genes connected to all types of cancer. One way to assess the performance of the BiLSTM model is through experiments on the database. On the other hand, enrichment analysis, survival analysis, and other outcomes can be used to confirm the biological importance of the prediction results. You may access the whole experimental protocols and programs at https://github.com/zhuyuan-cug/AI-BiLSTM/tree/master.
Improved two-photon photopolymerisation and optical trapping with aberration-corrected structured light
Authors: Armstrong D. J. , Stilgoe A. B , Nieminen T. A. , Rubinsztein-Dunlop H.
Published: October 2022

We demonstrate the effectiveness of phase only aberration corrections of structured light and their application to versatile optical trapping setups. We calculate phase corrections before (ex-situ) and after (in-situ) a high numerical aperture microscope objective using a spatial light modulator (SLM), and investigate how these corrections can be used to improve the efficiency and resolution of micro-structures fabricated through two-photon-photopolymerisation (2PP). We apply a phase retrieval algorithm to correct for distortions in a femtosecond laser that enables the fabrication of 3D structures using as many as 50 simultaneous foci. The inclusion of aberration correction in the fabrication process shows improved confinement of optically trapped particles and more efficient polymerisation while minimising intensity variations at individual foci, which potentially damage the structure during fabrication. We find that phase corrections allow for consistent voxel sizes, increased sharpness, and an expanded effective printing range when using an SLM, while also allowing for closer proximity of individual trap foci, minimising interference effects that hinder fabrication resolution.
Sex-specific behavioral outcomes of early-life adversity and emerging microglia-dependent mechanisms
Authors: Garvin Madison M. , Bolton Jessica L.
Published: October 2022

Early-life adversity (ELA) is known to alter brain circuit maturation as well as increase vulnerability to cognitive and emotional disorders. However, the importance of examining sex as a biological variable when researching the effects of ELA has not been considered until recently. This perspective discusses the sex-specific behavioral outcomes of ELA in both humans and animal models, then proposes microglia-mediated mechanisms as a potential underlying cause. Recent work in rodent models suggests that ELA provokes cognitive deficits, anhedonia, and alcohol abuse primarily in males, whereas females exhibit greater risk-taking and opioid addiction-related behaviors. In addition, emerging evidence identifies microglia as a key target of ELA. For example, we have recently shown that ELA inhibits microglial synapse engulfment and process dynamics in male mice, leading to an increase in excitatory synapse number onto corticotrophin-releasing hormone (CRH)-expressing neurons in the paraventricular nucleus of the hypothalamus (PVN) and aberrant stress responses later in life. However, ELA-induced synaptic rewiring of neural circuits differs in females during development, resulting in divergent behavioral outcomes. Thus, examining the role of microglia in the sex-specific mechanisms underlying ELA-induced neuropsychiatric disorders is an important topic for future research.
Assessment of time irreversibility in a time series using visibility graphs
Authors: Andrzejewska Małgorzata , Żebrowski Jan J. , Rams Karolina , Ozimek Mateusz , Baranowski Rafał
Published: October 2022

In this paper, we studied the time-domain irreversibility of time series, which is a fundamental property of systems in a nonequilibrium state. We analyzed a subgroup of the databases provided by University of Rochester, namely from the THEW Project. Our data consists of LQTS (Long QT Syndrome) patients and healthy persons. LQTS may be associated with an increased risk of sudden cardiac death (SCD), which is still a big clinical problem. ECG-based artificial intelligence methods can identify sudden cardiac death with a high accuracy. It follows that heart rate variability contains information about the possibility of SCD, which may be extracted, provided that appropriate methods are developed for this purpose. Our aim was to assess the complexity of both groups using visibility graph (VG) methods. Multivariate analysis of connection patterns of graphs built from time series was performed using multiplex visibility graph methods. For univariate time series, time irreversibility of the ECG interval QT of patients with LQTS was lower than for the healthy. However, we did not observe statistically significant difference in the comparison of RR intervals time series of the two groups studied. The connection patterns retrieved from multiplex VGs have more similarity with each other in the case of LQTS patients. This observation may be used to develop better methods for SCD risk stratification.
The effects of augmenting traditional rehabilitation with audio biofeedback in people with persistent imbalance following mild traumatic brain injury
Authors: Campbell Kody R. , Peterka Robert J. , Fino Peter C. , Parrington Lucy , Wilhelm Jennifer L. , Pettigrew Natalie C. , King Laurie A.
Published: October 2022

Complaints of non-resolving imbalance are common in individuals with chronic mild traumatic brain injury (mTBI). Vestibular rehabilitation therapy may be beneficial for this population. Additionally, wearable sensors can enable biofeedback, specifically audio biofeedback (ABF), and aid in retraining balance control mechanisms in people with balance impairments. In this study, we described the effectiveness of vestibular rehabilitation therapy with and without ABF to improve balance in people with chronic mTBI. Participants (n = 31; females = 22; mean age = 40.9 ± 11 y) with chronic (>3 months) mTBI symptoms of self-reported imbalance were randomized into vestibular rehabilitation with ABF (n = 16) or without ABF (n = 15). The intervention was a standard vestibular rehabilitation, with or without ABF, for 45 min biweekly for 6 weeks. The ABF intervention involved a smartphone that provided auditory feedback when postural sway was outside of predetermined equilibrium parameters. Participant's completed the Post-Concussion Symptom Scale (PCSS). Balance was assessed with the sensory organization test (SOT) and the Central Sensorimotor Integration test which measured sensory weighting, motor activation, and time delay with sway evoked by surface and/or visual surround tilts. Effect sizes (Hedge's G) were calculated on the change between pre-and post-rehabilitation scores. Both groups demonstrated similar medium effect-sized decreases in PCSS and large increases in SOT composite scores after rehabilitation. Effect sizes were minimal for increasing sensory weighting for both groups. The with ABF group showed a trend of larger effect sizes in increasing motor activation (with ABF = 0.75, without ABF = 0.22) and in decreasing time delay (with ABF = −0.77, without ABF = −0.52) relative to the without ABF group. Current clinical practice focuses primarily on sensory weighting. However, the evaluation and utilization of motor activation factors in vestibular rehabilitation, potentially with ABF, may provide a more complete assessment of recovery and improve outcomes.
Case report: Vaccine-induced immune thrombotic thrombocytopenia complicated by acute cerebral venous thrombosis and hemorrhage after AstraZeneca vaccines followed by Moderna COVID-19 vaccine booster and surgery
Authors: Chen Quan-Ting , Liu Yi , Chen Yeu-Chin , Chou Chung-Hsing , Lin Yu-Pang , Lin Yun-Qian , Tsai Ming-Chen , Chang Bo-Kang , Ho Tsung-Han , Lu Chun-Chi , Sung Yueh-Feng
Published: October 2022

Vaccine-induced thrombotic thrombocytopenia (VITT) is a well-known complication of adenoviral vector COVID-19 vaccines including ChAdOx1 nCoV-19 (AstraZeneca) and Ad26. COV2.S (Janssen, Johnson & Johnson). To date, only a few cases of mRNA COVID-19 vaccine such as mRNA-1273 (Moderna) or BNT162b2 (Pfizer-BioNTech)-induced VITT have been reported. We report a case of VITT with acute cerebral venous thrombosis and hemorrhage after a booster of mRNA-1273 (Moderna) vaccine in a patient previously vaccinated with two doses of the AstraZeneca vaccine. A 42-year-old woman presented with sudden onset of weakness of the right upper limb with focal seizure. She had received two doses of AstraZeneca vaccines and a booster with Moderna vaccine 32 days before presentation. She had also undergone a laparoscopic myomectomy 12 days previously. Laboratory examinations revealed anemia (9.5 g/dl), thrombocytopenia (31 × 103/μl), and markedly elevated d-dimer (>20.0 mg/L; reference value < 0.5 mg/L). The initial brain computed tomography (CT) was normal, but a repeated scan 10 h later revealed hemorrhage at the left cerebrum. Before the results of the blood smear were received, on suspicion of thrombotic microangiopathy with thrombocytopenia and thrombosis, plasmapheresis and pulse steroid therapy were initiated, followed by intravenous immunoglobulin (1 g/kg/day for two consecutive days) due to refractory thrombocytopenia. VITT was confirmed by positive anti-PF4 antibody and both heparin-induced and PF4-induced platelet activation testing. Clinicians should be aware that mRNA-1273 Moderna, an mRNA-based vaccine, may be associated with VITT with catastrophic complications. Additionally, prior exposure to the AstraZeneca vaccine and surgical procedure could also have precipitated or aggravated autoimmune heparin-induced thrombocytopenia/VITT-like presentation.
Case report: Endovascular embolization of a cerebral pseudoaneurysm caused by SARS-CoV2 infection
Authors: García-Carmona Juan Antonio , von Quednow Enzo , Hernández-Fernández Francisco , Molina-Nuevo Juan David , García-García Jorge , Palao María , Segura Tomás
Published: October 2022

Background

Severe COVID-19 has been shown to produce convulsions, encephalitis, Guillain-Barré syndrome, or cerebrovascular disease. However, only 4 case reports described subarachnoid or brain hemorrhage caused by ruptured cerebral aneurysms or pseudoaneurysms in patients with COVID-19. Cerebral pseudoaneurysms represent <1% of all intracranial aneurysms and have been related to radiation therapy, vasculitis, rupture of true saccular aneurysms, arteriovenous malformations, and infections by bacteria and viruses, such as Epstein-Bar and Herpes virus.

Case presentation

A 28-year-old Caucasian woman, with no medical history of interest and completely vaccinated against SARS-CoV-2, was admitted to Neurology due to progressive tetraparesis with areflexia, a cough, and a fever of 38°C. SARS-CoV2 PCR was positive while lumbar puncture, blood tests, and electromyogram showed criteria for Guillain-Barré syndrome. Despite the treatment, the patient developed dyspnea and tetraplegia requiring invasive mechanical ventilation. There was motor neurological improvement but a decreased level of consciousness was observed on day 13. A brain CT scan demonstrated an acute haematoma and cerebral arteriography showed a 4-mm pseudoaneurysm located in a branch of the left middle cerebral artery. Given the high risk of rebleeding, endovascular treatment was decided upon. Therefore, complete embolization of the pseudoaneurysm was carried out by using the synthetic glue N-butyl-cyanocrylate. Two days later, the patient was clinically and neurologically recovered and was discharged. Lastly, a new angiography showed no evidence of the pseudoaneurysm 3-weeks later.

Conclusions

We report, for the first time, a patient suffering a severe immune reaction caused by SARS-CoV2 infection and developing a cerebral pseudoaneurysm treated with endovascular embolization without complications.
Aberrant interhemispheric functional reciprocities of the default mode network and motor network in subcortical ischemic stroke patients with motor impairment: A longitudinal study
Authors: Li Yongxin , Yu Zeyun , Zhou Xuan , Wu Ping , Chen Jiaxu
Published: October 2022

Purpose

The purpose of the present study was to explore the longitudinal changes in functional homotopy in the default mode network (DMN) and motor network and its relationships with clinical characteristics in patients with stroke.

Methods

Resting-state functional magnetic resonance imaging was performed in stroke patients with subcortical ischemic lesions and healthy controls. The voxel-mirrored homotopic connectivity (VMHC) method was used to examine the differences in functional homotopy in patients with stroke between the two time points. Support vector machine (SVM) and correlation analyses were also applied to investigate whether the detected significant changes in VMHC were the specific feature in patients with stroke.

Results

The patients with stroke had significantly lower VMHC in the DMN and motor-related regions than the controls, including in the precuneus, parahippocampus, precentral gyrus, supplementary motor area, and middle frontal gyrus. Longitudinal analysis revealed that the impaired VMHC of the superior precuneus showed a significant increase at the second time point, which was no longer significantly different from the controls. Between the two time points, the changes in VMHC in the superior precuneus were significantly correlated with the changes in clinical scores. SVM analysis revealed that the VMHC of the superior precuneus could be used to correctly identify the patients with stroke from the controls with a statistically significant accuracy of 81.25% (P ≤ 0.003).

Conclusions

Our findings indicated that the increased VMHC in the superior precuneus could be regarded as the neuroimaging manifestation of functional recovery. The significant correlation and the discriminative power in classification results might provide novel evidence to understand the neural mechanisms responsible for brain reorganization after stroke.