bluuebunny/crossref_metadata_2025 huggingface dataset:
Evaluation of new robust silk fibroin hydrogels for posterior scleral reinforcement in rabbits
Authors: Xu Yule , Chen Qiaolin , Shao Zhengzhong , Wei Jiahong , Zhu Xuyou , Rong Ao , Chen Xin , Ni Yusu , Jiang Yi
Published: June 2023

Background: Currently, there is no ideal material available for posterior scleral reinforcement (PSR) to prevent the progression of high myopia. In this study, we investigated robust regenerated silk fibroin (RSF) hydrogels as potential grafts for PSR in animal experiments to evaluate their safety and biological reactions.

Methods: PSR surgery was performed on the right eye of twenty-eight adult New Zealand white rabbits, with the left eye serving as a self-control. Ten rabbits were observed for 3 months, while 18 rabbits were observed for 6 months. The rabbits were evaluated using intraocular pressure (IOP), anterior segment and fundus photography, A- and B-ultrasound, optical coherence tomography (OCT), histology, and biomechanical tests.

Results: No complications such as significant IOP fluctuation, anterior chamber inflammation, vitreous opacity, retinal lesion, infection, or material exposure were observed. Furthermore, no evidence of pathological changes in the optic nerve and retina, or structural abnormalities on OCT, were found. The RSF grafts were appropriately located at the posterior sclera and enclosed in fibrous capsules. The scleral thickness and collagen fiber content of the treated eyes increased after surgery. The ultimate stress of the reinforced sclera increased by 30.7%, and the elastic modulus increased by 33.0% compared to those of the control eyes at 6 months after surgery.

Conclusion: Robust RSF hydrogels exhibited good biocompatibility and promoted the formation of fibrous capsules at the posterior sclera in vivo. The biomechanical properties of the reinforced sclera were strengthened. These findings suggest that RSF hydrogel is a potential material for PSR.
Antimicrobial resistance and mechanisms of epigenetic regulation
Authors: Wang Xinrui , Yu Donghong , Chen Lu
Published: June 2023

The rampant use of antibiotics in animal husbandry, farming and clinical disease treatment has led to a significant issue with pathogen resistance worldwide over the past decades. The classical mechanisms of resistance typically investigate antimicrobial resistance resulting from natural resistance, mutation, gene transfer and other processes. However, the emergence and development of bacterial resistance cannot be fully explained from a genetic and biochemical standpoint. Evolution necessitates phenotypic variation, selection, and inheritance. There are indications that epigenetic modifications also play a role in antimicrobial resistance. This review will specifically focus on the effects of DNA modification, histone modification, rRNA methylation and the regulation of non-coding RNAs expression on antimicrobial resistance. In particular, we highlight critical work that how DNA methyltransferases and non-coding RNAs act as transcriptional regulators that allow bacteria to rapidly adapt to environmental changes and control their gene expressions to resist antibiotic stress. Additionally, it will delve into how Nucleolar-associated proteins in bacteria perform histone functions akin to eukaryotes. Epigenetics, a non-classical regulatory mechanism of bacterial resistance, may offer new avenues for antibiotic target selection and the development of novel antibiotics.
Bibliometric analysis of international publication trends on social media and terrorism by using the Scopus database
Authors: Yumitro Gonda , Febriani Rizki , Roziqin Ali , Indraningtyas Anisa
Published: June 2023

Social Media and Terrorism are often studied together and have become the focus of many authors in recent years. Therefore, this study aims to evaluate international publication trends on social media and terrorism, using the Scopus database through bibliometric analysis from 2009 to 2022. Data visualization and analysis were conducted using Microsoft Excel and VOSviewer. The results showed that the international publications trend reached a peak in 2018, with 103 publications emphasizing various topics, such as social media, terrorism, Twitter, terrorist attacks, and several issues related to terrorist activities and digital platforms. The United States was also the most common country of publication with the highest number of affiliated authors. In addition, the authors with the most published documents were Tsikrika T. and Vrochidis S., with the majority of reports prioritizing social sciences. These results are expected to contribute to the novelty of previous studies on social media and terrorism.
High anti-Mullerian hormone level is adversely associated with cumulative live birth rates of two embryo transfers after the first initiated cycle in patients with polycystic ovary syndrome
Authors: Su Nianjun , Zhan Juanxiao , Xie Meiling , Zhao Ying , Huang Cuiyu , Wang Songlu , Liao Liujun , Zhang Xiqian , Liu Fenghua
Published: June 2023

Objective

Anti-Mullerian hormone (AMH) has been recently identified as a potential predictor of live birth rates (LBRs) following assisted reproductive technology (ART) treatment. This study aimed to investigate the association between AMH levels and the outcomes of in vitro fertilization (IVF) in patients with polycystic ovary syndrome (PCOS).

Methods

Patients with PCOS initiating their first ovarian stimulation under the gonadotropin-releasing hormone antagonist protocol at the Guangdong Women and Children Hospital, China, were enrolled from November 2014 to September 2018. A total of 157 patients who underwent fresh embryo transfer (ET) cycles were included in group A, whereas 187 patients who underwent frozen–thawed ET cycles were included in group B. After the failure of the first ET cycle, 94 patients underwent the second ET cycle with frozen–thawed embryos. Of these 94 patients, 52 had failed the first fresh ET cycle (group C) and 42 had failed the first frozen–thawed ET cycle (group D). Successful embryo transfer was defined as live birth. This retrospective cohort study addressed the association between AMH levels and pregnancy outcomes using logistic regression approaches. After adjusting for age, body mass index, antral follicle counts, baseline follicle-stimulating hormone levels and baseline progesterone levels, LBRs were compared among the four groups and the cumulative live birth rate after two embryo transfers (TCLBR) was calculated.

Results

The LBRs showed no differences among the four groups. Higher serum AMH levels were found to be associated with a lower TCLBR [adjusted OR 0.937 (0.888–0.987), P = 0.015]. In patients who underwent the second ET cycle, LBRs were inversely proportional to AMH levels [crude OR 0.904 (0.828–0.986), P = 0.022 versus adjusted OR 0.845 (0.754–0.946), P = 0.004, respectively]. In addition, the LBR was approximately 61%–78% lower in the group with AMH levels of >12 ng/mL [crude OR 0.391 (0.168–0.912), P = 0.030 versus adjusted OR 0.217 (0.074–0.635), P = 0.005, respectively].

Conclusions

Among PCOS patients high AMH level (>12 ng/ml) is found to be associated with low TCLBR and low LBR of the second embryo transfer cycles. The results provide limited clinical inferences and warrant further investigation.
A camera trap method for estimating target densities of grey squirrels to inform wildlife management applications
Authors: Beatham Sarah E. , Stephens Philip A. , Coats Julia , Phillips John , Massei Giovanna
Published: June 2023

Effective wildlife population management requires an understanding of the abundance of the target species. In the United Kingdom, the increase in numbers and range of the non-native invasive grey squirrel Sciurus carolinensis poses a substantial threat to the existence of the native red squirrel S. vulgaris, to tree health, and to the forestry industry. Reducing the number of grey squirrels, is crucial to mitigate their impacts. Camera traps are increasingly used to estimate animal abundance, and methods have been developed that do not require the identification of individual animals. Most of these methods have been focussed on medium to large mammal species with large range sizes and may be unsuitable for measuring local abundances of smaller mammals that have variable detection rates and hard to measure movement behaviour. The aim of this study was to develop a practical and cost-effective method, based on a camera trap index, that could be used by practitioners to estimate target densities of grey squirrels in woodlands to provide guidance on the numbers of traps or contraceptive feeders required for local grey squirrel control. Camera traps were deployed in ten independent woods of between 6 and 28 ha in size. An index, calculated from the number of grey squirrel photographs recorded per camera per day had a strong linear relationship (R2 = 0.90) with the densities of squirrels removed in trap and dispatch operations. From different time filters tested, a 5 min filter was applied, where photographs of squirrels recorded on the same camera within 5 min of a previous photograph were not counted. There were no significant differences between the number of squirrel photographs per camera recorded by three different models of camera, increasing the method’s practical application. This study demonstrated that a camera index could be used to inform the number of feeders or traps required for grey squirrel management through culling or contraception. Results could be obtained within 6 days without requiring expensive equipment or a high level of technical input. This method can easily be adapted to other rodent or small mammal species, making it widely applicable to other wildlife management interventions.
Predicting fish species richness and abundance in the Lower Mekong Basin
Authors: Ngor Peng Bun , Uy Sophorn , Sor Ratha , Chan Bunyeth , Holway Joseph , Null Sarah E. , So Nam , Grenouillet Gaël , Chandra Sudeep , Hogan Zeb S. , Lek Sovan
Published: June 2023

Predictive models are widely used to investigate relationships between the distribution of fish diversity, abundance, and the environmental conditions in which they inhabit, and can guide management actions and conservation policies. Generally, the framework to model such relationships is established; however, which models perform best in predicting fish diversity and abundance remain unexplored in the Mekong River Basin. Here, we evaluated the performance of six single statistical models namely Generalized Linear Model, Classification and Regression Tree, Artificial Neural Network, k-Nearest Neighbor, Support Vector Machine and Random Forest in predicting fish species richness and abundance in the Lower Mekong Basin. We also identified key variables explaining variability and assessed the variable’s sensitivity in prediction of richness and abundance. Moreover, we explored the usefulness of an ensemble modeling approach and investigated if this approach improved model performance. Our results indicated that, overall, the six single statistical models successfully predicted the fish species richness and abundance using 14 geo-hydrological, physicochemical and climatic variables. The Random Forest model consistently out-performed all single statistical models for predicting richness (R2 = 0.85) and abundance (R2 = 0.77); whereas, Generalized Linear Model performed the worst of all models (R2 = 0.60 and 0.56 for richness and abundance). The most important predictors of variation in both richness and abundance included water level, distance from the sea and alkalinity. Additionally, dissolved oxygen, water temperature and total nitrate were important predictors of species richness, while conductivity was important for fish abundance. We found that species richness increased with increasing water level, dissolved oxygen and water temperature, but decreased with increasing distance from the sea, alkalinity and total nitrate. Fish abundance increased with conductivity, but decreased with increasing distance from the sea, water level and alkalinity. Finally, our results highlighted the usefulness of ensemble modeling (R2 = 0.90 and 0.85 for richness and abundance) for providing better predictive power than any of the six single statistical models. Our results can be used to support Mekong River management, particularly fisheries in the context of contemporary regional and global changes.
A remote sensing approach to assess the historical invasion of Phragmites australis in a brackish coastal marsh
Authors: Hagani Jason S. , Takekawa John Y. , Chappell Steven C. , Tanner Richelle L. , Ernst Adrienne R. , Kettenring Karin M.
Published: June 2023

Introduction

Coastal estuarine wetlands provide important habitats for a variety of endemic flora and fauna but are particularly vulnerable to biological invasions. Regular monitoring of changes in these vulnerable wetlands has become increasingly important for effective management, especially considering threats from climate change effects and human disturbance. Historical analyzes of plant invasions may guide targeted management strategies to eradicate harmful species. Estimating the distribution of invasive species has never been more accessible with the improved availability of high-resolution data and innovations in remote sensing, estimating the distribution of invasive species has never been more accessible.

Methods

We assessed the spread of non-native Phragmites australis subsp. australis in Suisun Marsh on the upper San Francisco Estuary, one of the largest brackish coastal wetlands in North America. Suisun Marsh consists of managed and tidal wetlands, and efforts have been made to control invasive P. australis on the managed wetlands to support habitat values for wildlife. We used remote-sensing analyzes of publicly available, biennial color-infrared images taken by the National Agriculture Imagery Program (NAIP) to map the expansion of invasive P. australis across two decades. We generated random forest classifications of representative images to map the distribution of P. australis, then calculated a variety of metrics describing the rate and spatial extent of the P. australis spread. Additionally, we ran generalized linear models to examine factors related to the growth of P. australis.

Results

Our classifications yielded accuracies of over 90% and showed a 234% (1,084 ha) increase in P. australis between 2003 and 2018. The expansion rate of P. australis patches averaged 1.32 m/year (±0.53 SD) which is higher than most reported in the literature. We found that P. australis expansion in managed areas within levees was significantly correlated with invasion in tidal areas outside the levees on the same parcel and also related to its spread on adjacent parcels.

Discussion

Our findings suggest that despite individual landowner management efforts, P. australis has continued to expand substantially throughout Suisun Marsh. Future efforts to treat invasive P. australis may require emphasizing adaptive, collaborative management rather than individual management strategies to ensure the invasive species is eradicated on a large scale to preserve the valued ecosystem functions.
Immunodeficiency with susceptibility to lymphoma with complex genotype affecting energy metabolism (FBP1, ACAD9) and vesicle trafficking (RAB27A)
Authors: Brauer Nina , Maruta Yuto , Lisci Miriam , Strege Katharina , Oschlies Ilske , Nakamura Hikari , Böhm Svea , Lehmberg Kai , Brandhoff Leon , Ehl Stephan , Parvaneh Nima , Klapper Wolfram , Fukuda Mitsunori , Griffiths Gillian M. , Hennies Hans Christian , Niehues Tim , Ammann Sandra
Published: June 2023

Introduction

Inborn errors of immunity (IEI) are characterized by a dysfunction of the immune system leading to increased susceptibility to infections, impaired immune regulation and cancer. We present a unique consanguineous family with a history of Hodgkin lymphoma, impaired EBV control and a late onset hemophagocytic lymphohistiocytosis (HLH).

Methods and results

Overall, family members presented with variable impairment of NK cell and cytotoxic T cell degranulation and cytotoxicity. Exome sequencing identified homozygous variants in RAB27A, FBP1 (Fructose-1,6-bisphosphatase 1) and ACAD9 (Acyl-CoA dehydrogenase family member 9). Variants in RAB27A lead to Griscelli syndrome type 2, hypopigmentation and HLH predisposition.

Discussion

Lymphoma is frequently seen in patients with hypomorphic mutations of genes predisposing to HLH. We hypothesize that the variants in FBP1 and ACAD9 might aggravate the clinical and immune phenotype, influence serial killing and lytic granule polarization by CD8 T cells. Understanding of the interplay between the multiple variants identified by whole exome sequencing (WES) is essential for correct interpretation of the immune phenotype and important for critical treatment decisions.
Incidence and risk factors of tuberculosis in systemic lupus erythematosus patients: a multi-center prospective cohort study
Authors: Zhang Lifan , Zou Xiaoqing , Jiang Nan , Xie Lantian , Liu Jianghao , Yang Zhengrong , Cao Qifei , Li Chunlei , Sun Xiaochuan , Zhang Fengchun , Zhao Yan , Zeng Xiaofeng , Shi Xiaochun , Liu Xiaoqing ,   for the ETHERTB study team
Published: June 2023

Objectives

Both burdens of tuberculosis (TB) and systemic lupus erythematosus (SLE) in China are ranked as top three in the world. SLE patients are at high risk for TB, but so far, there are no guidelines for TB prevention and management targeting this population in China. This study aims to investigate the incidence of active tuberculosis (ATB) and to explore the risk factors for developing ATB in SLE patients, and to provide evidence for TB prevention and management for SLE patients in China.

Methods

A multi-center prospective cohort study was conducted. SLE patients were enrolled from clinics and wards of 13 tertiary hospitals in Eastern, Middle, and Western China from September 2014 to March 2016. Baseline demographic features, TB infection status, clinical information, and laboratory data were collected. ATB development was examined during follow-up visits. Kaplan-Meier method was applied to plot survival curves, and Log-rank test was used to evaluate differences. Cox proportional-hazards model was used to explore the risk factors for ATB development.

Results

With a median follow-up time of 58 months [interquartile range (IQR): 55-62], 16 out of 1361 SLE patients developed ATB. The 1-year incidence of ATB was 368 [95% confidence interval (CI): 46-691] per 100,000. Over a 5-year period, the cumulative incidence of ATB was 1141 [95% CI: 564-1718] per 100,000, and the incidence density was 245 per 100,000 person-years. Cox regression models were constructed with maximum daily dose of glucocorticoids (GCs) as a continuous variable and a categorical variable, respectively. In model 1, maximum daily dose of GCs (pills per day) [adjusted hazard ratio (aHR)=1.16, 95%CI: 1.04-1.30, p=0.010] and TB infection (aHR=8.52, 95%CI: 3.17-22.92, p<0.001) were independent risk factors for ATB development. In model 2, maximum daily dose of GCs≥30 mg/d (aHR =4.81, 95%CI: 1.09-22.21, P=0.038) and TB infection (aHR=8.55, 95%CI: 3.18-23.00, p<0.001] were independent risk factors for ATB development.

Conclusions

SLE patients had a higher incidence of ATB compared to the general population. The risk of developing ATB was even higher with increased daily dose of GCs or in a status of TB infection, in which case TB preventive treatment should be considered.
Plasma glycoproteomic biomarkers identify metastatic melanoma patients with reduced clinical benefit from immune checkpoint inhibitor therapy
Authors: Pickering Chad , Aiyetan Paul , Xu Gege , Mitchell Alan , Rice Rachel , Najjar Yana G. , Markowitz Joseph , Ebert Lisa M. , Brown Michael P. , Tapia-Rico Gonzalo , Frederick Dennie , Cong Xin , Serie Daniel , Lindpaintner Klaus , Schwarz Flavio , Boland Genevieve M.
Published: June 2023

The clinical success of immune-checkpoint inhibitors (ICI) in both resected and metastatic melanoma has confirmed the validity of therapeutic strategies that boost the immune system to counteract cancer. However, half of patients with metastatic disease treated with even the most aggressive regimen do not derive durable clinical benefit. Thus, there is a critical need for predictive biomarkers that can identify individuals who are unlikely to benefit with high accuracy so that these patients may be spared the toxicity of treatment without the likely benefit of response. Ideally, such an assay would have a fast turnaround time and minimal invasiveness. Here, we utilize a novel platform that combines mass spectrometry with an artificial intelligence-based data processing engine to interrogate the blood glycoproteome in melanoma patients before receiving ICI therapy. We identify 143 biomarkers that demonstrate a difference in expression between the patients who died within six months of starting ICI treatment and those who remained progression-free for three years. We then develop a glycoproteomic classifier that predicts benefit of immunotherapy (HR=2.7; p=0.026) and achieves a significant separation of patients in an independent cohort (HR=5.6; p=0.027). To understand how circulating glycoproteins may affect efficacy of treatment, we analyze the differences in glycosylation structure and discover a fucosylation signature in patients with shorter overall survival (OS). We then develop a fucosylation-based model that effectively stratifies patients (HR=3.5; p=0.0066). Together, our data demonstrate the utility of plasma glycoproteomics for biomarker discovery and prediction of ICI benefit in patients with metastatic melanoma and suggest that protein fucosylation may be a determinant of anti-tumor immunity.
High DNA methylation age deceleration defines an aggressive phenotype with immunoexclusion environments in endometrial carcinoma
Authors: Hao Jing , Liu Tiantian , Xiu Yuchen , Yuan Huiyang , Xu Dawei
Published: June 2023

Like telomere shortening, global DNA hypomethylation occurs progressively with cellular divisions or in vivo aging and functions as a mitotic clock to restrain malignant transformation/progression. Several DNA-methylation (DNAm) age clocks have been established to precisely predict chronological age using normal tissues, but show DNAm age drift in tumors, which suggests disruption of this mitotic clock during carcinogenesis. Little is known about DNAm age alterations and biological/clinical implications in endometrial cancer (EC). Here we address these issues by analyzing TCGA and GSE67116 cohorts of ECs. Horvath clock analysis of these tumors unexpectedly revealed that almost 90% of them exhibited DNAm age deceleration (DNAmad) compared to patient chronological age. Combined with an additional clock named Phenoage, we identified a subset of tumors (82/429) with high DNAmad (hDNAmad+) as assessed by both clocks. Clinically, hDNAmad+ tumors were associated with advanced diseases and shorter patient survival, compared to hDNAmad- ones. Genetically, hDNAmad+ tumors were characterized by higher copy number alterations (CNAs) whereas lower tumor mutation burden. Functionally, hDNAmad+ tumors were enriched with cell cycle and DNA mismatch repair pathways. Increased PIK3CA alterations and downregulation of SCGB2A1, the inhibitor of PI3K kinase, in hDNAmad+ tumors, might promote tumor growth/proliferation and stemness. In addition, the inactivation of aging drivers/tumor suppressors (TP53, RB1, and CDKN2A) while enhanced telomere maintenance occurred more frequently in hDNAmad+ tumors, which supports sustained tumor growth. Prominently, hDNAmad+ tumors were featured with immunoexclusion microenvironments, accompanied by significantly higher levels of VTCN1 expression while lower PD-L1 and CTLA4 expression, which indicates their poor response to immune checkpoint inhibitor (ICI)-based immunotherapy. We further showed significantly higher levels of DNMT3A and 3B expression in hDNAmad+ than in hDNAmad- tumors. Thus, the tumor suppressive function of aging-like DNA hypomethylation is severely impaired in hDNAmad+ tumors, likely due to enhanced expression of DNMT3A/3B and dysregulated aging regulators. Our findings not only enrich biological knowledge of EC pathogenesis but also help improve EC risk stratification and precision ICI immunotherapy.
Effect of shear ratio on rheological properties of suspension in two-step flocculation process for fine iron tailings
Authors: Yang Ying , Wu Aixiang , Wang Xiancheng , Wang Guoli
Published: June 2023

In the two-step flocculation process, shear has a significant impact on the rheological properties of the flocculating slurry. In this study, the orthogonal experiments of two-step flocculation process for fine iron tailings were designed. Based on the change of shear ratio, different shear rates and shear time were designed, the yield stress, plastic viscosity and maximum packing fraction of the flocculated suspension in each group were measured and calculated with a rheometer. The result of range and variance analysis shows the shear rate in the primary broken phase was the biggest factor affecting the yield stress and plastic viscosity of the flocculated slurry in two-step flocculation process. When the shear rate increased from 100 s-1 to 400 s-1, the yield stress and the plastic viscosity of the flocculated slurry increased by 7.14% and 21.30%, respectively. When the shear rate changed from 400 s-1 to 800 s-1, they decreased by 23.27% and 33.17%, respectively. Since the shear ratio in a two-step flocculation process is also related to both shear action and floc structure parameter, the shear ratio was introduced into the first-order reversible kinetic rate equation. Through establishing the relationship between the shear ratio and the floc structural parameter of flocculating suspension, a theoretical model of the shear-dependent maximum packing fraction was established. The measured values and theoretical calculated values of the maximum packing fraction in two-step flocculation experiments were in good agreement and the error was within 5%. Last but not least, the internal mechanism of the theoretical model was discussed from the microscopic point of view.
Screening microbial inoculants and their interventions for cross-kingdom management of wilt disease of solanaceous crops- a step toward sustainable agriculture
Authors: Kashyap Abhijeet Shankar , Manzar Nazia , Meshram Shweta , Sharma Pawan Kumar
Published: June 2023

Microbial inoculants may be called magical bullets because they are small in size but have a huge impact on plant life and humans. The screening of these beneficial microbes will give us an evergreen technology to manage harmful diseases of cross-kingdom crops. The production of these crops is reducing as a result of multiple biotic factors and among them the bacterial wilt disease triggered byRalstonia solanacearumis the most important in solanaceous crops. The examination of the diversity of bioinoculants has shown that more microbial species have biocontrol activity against soil-borne pathogens. Reduced crop output, lower yields, and greater cost of cultivation are among the major issues caused by diseases in agriculture around the world. It is universally true that soil-borne disease epidemics pose a greater threat to crops. These necessitate the use of eco-friendly microbial bioinoculants. This review article provides an overview of plant growth-promoting microorganisms bioinoculants, their various characteristics, biochemical and molecular screening insights, and modes of action and interaction. The discussion is concluded with a brief overview of potential future possibilities for the sustainable development of agriculture. This review will be useful for students and researchers to obtain existing knowledge of microbial inoculants, their activities, and their mechanisms, which will facilitate the development of environmentally friendly management strategies for cross-kingdom plant diseases.
Precise and versatile microplate reader-based analyses of biosensor signals from arrayed microbial colonies
Authors: Hartmann Fabian S. F. , Weiß Tamara , Kastberg Louise L. B. , Workman Christopher T. , Seibold Gerd M.
Published: June 2023

Genetically encoded fluorescent biosensors have emerged as a powerful tool to support phenotypic screenings of microbes. Optical analyses of fluorescent sensor signals from colonies grown on solid media can be challenging as imaging devices need to be equipped with appropriate filters matching the properties of fluorescent biosensors. Toward versatile fluorescence analyses of different types of biosensor signals derived from arrayed colonies, we investigate here the use of monochromator equipped microplate readers as an alternative to imaging approaches. Indeed, for analyses of the LacI-controlled expression of the reporter mCherry in Corynebacterium glutamicum, or promoter activity using GFP as reporter in Saccharomyces cerevisiae, an improved sensitivity and dynamic range was observed for a microplate reader-based analyses compared to their analyses via imaging. The microplate reader allowed us to capture signals of ratiometric fluorescent reporter proteins (FRPs) with a high sensitivity and thereby to further improve the analysis of internal pH via the pH-sensitive FRP mCherryEA in Escherichia coli colonies. Applicability of this novel technique was further demonstrated by assessing redox states in C. glutamicum colonies using the FRP Mrx1-roGFP2. By the use of a microplate reader, oxidative redox shifts were measured in a mutant strain lacking the non-enzymatic antioxidant mycothiol (MSH), indicating its major role for maintaining a reduced redox state also in colonies on agar plates. Taken together, analyses of biosensor signals from microbial colonies using a microplate reader allows comprehensive phenotypic screenings and thus facilitates further development of new strains for metabolic engineering and systems biology.
The role of complex interactions between the intestinal flora and host in regulating intestinal homeostasis and inflammatory bowel disease
Authors: Li Siyu , Xu Kan , Cheng Yi , Chen Lu , Yi Ailin , Xiao Zhifeng , Zhao Xuefei , Chen Minjia , Tian Yuting , Meng Wei , Tang Zongyuan , Zhou Shuhong , Ruan Guangcong , Wei Yanling
Published: June 2023

Pharmacological treatment of inflammatory bowel disease (IBD) is inefficient and difficult to discontinue appropriately, and enterobacterial interactions are expected to provide a new target for the treatment of IBD. We collected recent studies on the enterobacterial interactions among the host, enterobacteria, and their metabolite products and discuss potential therapeutic options. Intestinal flora interactions in IBD are affected in the reduced bacterial diversity, impact the immune system and are influenced by multiple factors such as host genetics and diet. Enterobacterial metabolites such as SCFAs, bile acids, and tryptophan also play important roles in enterobacterial interactions, especially in the progression of IBD. Therapeutically, a wide range of sources of probiotics and prebiotics exhibit potential therapeutic benefit in IBD through enterobacterial interactions, and some have gained wide recognition as adjuvant drugs. Different dietary patterns and foods, especially functional foods, are novel therapeutic modalities that distinguish pro-and prebiotics from traditional medications. Combined studies with food science may significantly improve the therapeutic experience of patients with IBD. In this review, we provide a brief overview of the role of enterobacteria and their metabolites in enterobacterial interactions, discuss the advantages and disadvantages of the potential therapeutic options derived from such metabolites, and postulate directions for further research.
Radiotherapy-induced ferroptosis for cancer treatment
Authors: Beretta Giovanni L. , Zaffaroni Nadia
Published: June 2023

Ferroptosis is a regulated cell death mechanism controlled by iron, amino acid and reactive oxygen species metabolisms, which is very relevant for cancer therapy. Radiotherapy-induced ferroptosis is critical for tumor suppression and several preclinical studies have demonstrated that the combination of ionizing radiation with small molecules or nano-systems is effective in combating cancer growth and overcoming drug or ionizing radiation resistance. Here, we briefly overview the mechanisms of ferroptosis and the cross-talk existing between the cellular pathways activated by ferroptosis and those induced by radiotherapy. Lastly, we discuss the recently reported combinational studies involving radiotherapy, small molecules as well as nano-systems and report the recent findings achieved in this field for the treatment of tumors.
Nest-associated scent marks help bumblebees localizing their nest in visually ambiguous situations
Authors: Eckel Sonja , Egelhaaf Martin , Doussot Charlotte
Published: June 2023

Social insects such as ants and bees are excellent navigators. To manage their daily routines bumblebees, as an example, must learn multiple locations in their environment, like flower patches and their nest. While navigating from one location to another, they mainly rely on vision. Although the environment in which bumblebees live, be it a meadow or a garden, is visually stable overall, it may be prone to changes such as moving shadows or the displacement of an object in the scenery. Therefore, bees might not solely rely on visual cues, but use additional sources of information, forming a multimodal guidance system to ensure their return home to their nest. Here we show that the home-finding behavior of bumblebees, when confronted with a visually ambiguous scenario, is strongly influenced by natural scent marks they deposit at the inconspicuous nest hole when leaving their nest. Bumblebees search for a longer time and target their search with precision at potential nest locations that are visually familiar, if also marked with their natural scent. This finding sheds light on the crucial role of odor in helping bees find their way back to their inconspicuous nest.
Extracellular matrix composition affects outgrowth of dendrites and dendritic spines on cortical neurons
Authors: Sharma Archana , Hill Katherine E. , Schwarzbauer Jean E.
Published: June 2023

The composition of the extracellular matrix (ECM) in nervous tissue plays an important role in controlling neuronal outgrowth and synapse development. Changes in both protein and glycosaminoglycan components of the ECM occur with tissue injury and may affect neuron growth. To investigate neuron responses to alterations in fibronectin (FN), a major component of the wound ECM, we grew cortical neurons on cell-derived decellularized matrices composed of wild type FN (FN+/+) or of a mutant form of FN (FNΔ/+) from which the III13 heparin-binding site had been deleted by CRISPR-Cas 9 gene editing. The most significant effect of the mutant FN was a reduction in dendrite outgrowth. Not only were dendrites shorter on mutant FNΔ/+-collagen (COL) matrix than on wild type (FN+/+-COL) matrix, but the number of dendrites and dendritic spines per neuron and the spine densities were also dramatically reduced on FNΔ/+-COL matrices. Mass spectrometry and immunostaining identified a reduction in tenascin-C (TN-C) levels in the mutant matrix. TN-C is an ECM protein that binds to the III13 site of FN and modulates cell-matrix interactions and has been linked to dendrite development. We propose that TN-C binding to FN in the wound matrix supports dendrite and spine development during repair of damaged neural tissue. Overall, these results show that changes in ECM composition can dramatically affect elaboration of neurites and support the idea that the ECM microenvironment controls neuron morphology and connectivity.
Impact of non-neuronal cells in Alzheimer’s disease from a single-nucleus profiling perspective
Authors: Vu Tra-My , Hervé Vincent , Ulfat Anosha Kiran , Lamontagne-Kam Daniel , Brouillette Jonathan
Published: June 2023

The role of non-neuronal cells has been relatively overlooked in Alzheimer’s disease (AD) neuropathogenesis compared to neuronal cells since the first characterization of the disease. Genome wide-association studies (GWAS) performed in the last few decades have greatly contributed to highlighting the critical impact of non-neuronal cells in AD by uncovering major genetic risk factors that are found largely in these cell types. The recent development of single cell or single nucleus technologies has revolutionized the way we interrogate the transcriptomic and epigenetic profiles of neurons, microglia, astrocytes, oligodendrocytes, pericytes, and endothelial cells simultaneously in the same sample and in an individual manner. Here, we review the latest advances in single-cell/nucleus RNA sequencing and Assay for Transposase-Accessible Chromatin (ATAC) sequencing to more accurately understand the function of non-neuronal cells in AD. We conclude by giving an overview of what still needs to be achieved to better appreciate the interconnected roles of each cell type in the context of AD.
Association between hemoglobin-to-red blood cell distribution width ratio and hospital mortality in patients with non-traumatic subarachnoid hemorrhage
Authors: Liu Jiuling , Wang Junhong
Published: June 2023

Background

In patients with ischemic stroke, low hemoglobin-to-red blood cell distribution width ratio (HRR) was associated with an increased risk of mortality. However, it was unknown in the non-traumatic subarachnoid hemorrhage (SAH) population. The purpose of this study was to examine the association between baseline HRR and in-hospital mortality in patients with non-traumatic SAH.

Methods

Non-traumatic SAH patients were screened out of the Medical Information Mart for Intensive IV (MIMIC-IV) database between 2008 and 2019. The Cox proportional hazard regression models were utilized to analyze the association between baseline HRR and in-hospital mortality. Restricted cubic splines (RCS) analysis was utilized to determine the relationship curve between hospital mortality and the HRR level and examine the threshold saturation effect. We further applied Kaplan–Meier survival curve analysis to examine the consistency of these correlations. The interaction test was used to identify subgroups with differences.

Results

A total of 842 patients were included in this retrospective cohort study. Compared with individuals with lower HRR Q1 ( ≤ 7.85), the adjusted HR values in Q2 (7.86–9.15), Q3 (9.16–10.16), and Q4 (≥10.17) were 0.574 (95% CI: 0.368–0.896, p = 0.015), 0.555 (95% CI: 0.346–0.890, p = 0.016), and 0.625 (95% CI: 0.394–0.991, p = 0.045), respectively. The association between the HRR level and in-hospital mortality exhibited a non-linear relationship (p < 0.05). The threshold inflection point value of 9.50 was calculated using RCS analysis. When the HHR level was lower than 9.50, the risk of in-hospital mortality rate decreased with an adjusted HR of 0.79 (95% CI: 0.70–0.90, p = 0.0003). When the HRR level was higher than 9.50, the risk of in-hospital mortality almost hardly increased with the increase in the HRR level (adjusted HR = 1.18, 95% CI: 0.91–1.53, p = 0.2158). K-M analysis showed that patients with low HRR levels had significantly higher in-hospital mortality (p < 0.001).

Conclusion

There was a non-linear connection between the baseline HRR level and in-hospital mortality. A low level of HRR could increase the risk of death in participants with non-traumatic SAH.
Skull base reconstruction using in situ bone flap in patients with pituitary adenomas treated by endoscopic endonasal approach
Authors: Chen Kaile , Dai Kexiang , Liu Zhiyuan , Liu Jinlai , Yu Kuo , Lu Ailin , Zhao Peng
Published: June 2023

Objective

The objective of this study is to study the effect of in situ bone flap (ISBF) repositioning, a recently proposed rigid skull base reconstruction technique, on patients diagnosed with pituitary adenoma undergoing endoscopic endonasal approach (EEA).

Method

A retrospective analysis was conducted on 188 patients with pituitary adenomas who underwent EEA from February 2018 to September 2022. Patients were divided into the ISBF group and non-ISBF group, according to whether ISBF was used during skull base reconstruction.

Results

Of the 75 patients in the non-ISBF group, 6 had postoperative cerebrospinal fluid (CSF) leakage (8%), while only 1 of 113 patients in the ISBF group (0.8%) had postoperative CSF leakage, indicating that the incidence of postoperative CSF leakage in the ISBF group was significantly lower than that in the non-ISBF group (P = 0.033). In addition, we also found that the postoperative hospitalization days of patients in the ISBF group (5.34 ± 1.24) were significantly less than those in the non-ISBF group (6.83 ± 1.91, P = 0.015).

Conclusion

ISBF repositioning is a safe, effective, and convenient rigid skull base reconstruction method for patients with pituitary adenoma treated by EEA, which can significantly reduce the rate of postoperative CSF leakage and shorten postoperative hospital stays.
SNAP: a structure-based neuron morphology reconstruction automatic pruning pipeline
Authors: Ding Liya , Zhao Xuan , Guo Shuxia , Liu Yufeng , Liu Lijuan , Wang Yimin , Peng Hanchuan
Published: June 2023

Background

Neuron morphology analysis is an essential component of neuron cell-type definition. Morphology reconstruction represents a bottleneck in high-throughput morphology analysis workflow, and erroneous extra reconstruction owing to noise and entanglements in dense neuron regions restricts the usability of automated reconstruction results. We propose SNAP, a structure-based neuron morphology reconstruction pruning pipeline, to improve the usability of results by reducing erroneous extra reconstruction and splitting entangled neurons.

Methods

For the four different types of erroneous extra segments in reconstruction (caused by noise in the background, entanglement with dendrites of close-by neurons, entanglement with axons of other neurons, and entanglement within the same neuron), SNAP incorporates specific statistical structure information into rules for erroneous extra segment detection and achieves pruning and multiple dendrite splitting.

Results

Experimental results show that this pipeline accomplishes pruning with satisfactory precision and recall. It also demonstrates good multiple neuron-splitting performance. As an effective tool for post-processing reconstruction, SNAP can facilitate neuron morphology analysis.
Cry1 expression during postnatal development is critical for the establishment of normal circadian period
Authors: Schirmer Aaron E. , Kumar Vivek , Schook Andrew , Song Eun Joo , Marshall Michael S. , Takahashi Joseph S.
Published: June 2023

The mammalian circadian system generates an approximate 24-h rhythm through a complex autoregulatory feedback loop. Four genes, Period1 (Per1), Period2 (Per2), Cryptochrome1 (Cry1), and Cryptochrome2 (Cry2), regulate the negative feedback within this loop. Although these proteins have distinct roles within the core circadian mechanism, their individual functions are poorly understood. Here, we used a tetracycline trans-activator system (tTA) to examine the role of transcriptional oscillations in Cry1 and Cry2 in the persistence of circadian activity rhythms. We demonstrate that rhythmic Cry1 expression is an important regulator of circadian period. We then define a critical period from birth to postnatal day 45 (PN45) where the level of Cry1 expression is critical for setting the endogenous free running period in the adult animal. Moreover, we show that, although rhythmic Cry1 expression is important, in animals with disrupted circadian rhythms overexpression of Cry1 is sufficient to restore normal behavioral periodicity. These findings provide new insights into the roles of the Cryptochrome proteins in circadian rhythmicity and further our understanding of the mammalian circadian clock.
Spiking neural network with working memory can integrate and rectify spatiotemporal features
Authors: Chen Yi , Liu Hanwen , Shi Kexin , Zhang Malu , Qu Hong
Published: June 2023

In the real world, information is often correlated with each other in the time domain. Whether it can effectively make a decision according to the global information is the key indicator of information processing ability. Due to the discrete characteristics of spike trains and unique temporal dynamics, spiking neural networks (SNNs) show great potential in applications in ultra-low-power platforms and various temporal-related real-life tasks. However, the current SNNs can only focus on the information a short time before the current moment, its sensitivity in the time domain is limited. This problem affects the processing ability of SNN in different kinds of data, including static data and time-variant data, and reduces the application scenarios and scalability of SNN. In this work, we analyze the impact of such information loss and then integrate SNN with working memory inspired by recent neuroscience research. Specifically, we propose Spiking Neural Networks with Working Memory (SNNWM) to handle input spike trains segment by segment. On the one hand, this model can effectively increase SNN's ability to obtain global information. On the other hand, it can effectively reduce the information redundancy between adjacent time steps. Then, we provide simple methods to implement the proposed network architecture from the perspectives of biological plausibility and neuromorphic hardware friendly. Finally, we test the proposed method on static and sequential data sets, and the experimental results show that the proposed model can better process the whole spike train, and achieve state-of-the-art results in short time steps. This work investigates the contribution of introducing biologically inspired mechanisms, e.g., working memory, and multiple delayed synapses to SNNs, and provides a new perspective to design future SNNs.
A systematic review on the impact of gastrointestinal microbiota composition and function on cognition in healthy infants and children
Authors: McMath Arden L. , Aguilar-Lopez Miriam , Cannavale Corinne N. , Khan Naiman A. , Donovan Sharon M.
Published: June 2023

Evidence from animal models or children with neurodevelopmental disorders has implicated the gut microbiome (GM) in neurocognitive development. However, even subclinical impairement of cognition can have negative consequences, as cognition serves as the foundation for skills necessary to succeed in school, vocation and socially. The present study aims to identify gut microbiome characteristics or changes in gut microbiome characteristics that consistently associate with cognitive outcomes in healthy, neurotypical infants and children. Of the 1,520 articles identified in the search, 23 were included in qualitative synthesis after applying exclusion criteria. Most studies were cross-sectional and focused on behavior or motor and language skills. Bifidobacterium, Bacteroides, Clostridia, Prevotella, and Roseburia were related to these aspects of cognition across several studies. While these results support the role of GM in cognitive development, higher quality studies focused on more complex cognition are needed to understand the extent to which the GM contributes to cognitive development.