bluuebunny/crossref_metadata_2025 huggingface dataset:
Exploring the usage and impact of urban sanitation tools targeting low- and middle-income countries
Authors: Furlong C. , Mugendi A. , Brdjanovic D.
Published: July 2023

Background: In recent years the number of tools developed to help advance sustainable urban sanitation coverage in low- and middle-income countries has increased significantly, yet no study has been undertaken to determine their usage or impact. This paper explores the usage and impact of four urban sanitation tools: Shit flow Diagram (SFD), City Service Delivery Assessment (CSDA), SaniPath, and the Citywide Planning Tool.

Methods: A mixed methodology approach was used which included a questionnaire (n = 87) and interviewing the tools developers (n = 5) and users (n = 25).

Results and discussion: There was a high awareness of three of the tools (86%, n = 87), but relatively low usage (53%, n = 87). The questionnaire respondents and interviewees confused the Citywide Planning Tool with other tools, so no usage was found. The CSDA and SaniPath were being used beyond the groups that developed them and by their targeted group, but the main users were found to be researchers in academia. There was evidence that SFDs and CSDAs were evolving beyond their original scope, which was attributed to their use in academia. Their use in academia should not be dismissed as they may lead to future usage and impact. Although impact will take time and it is difficult to directly attribute impact to a specific tool, evidence of the impact of the SFD and SaniPath was found. This impact demonstrates how these tools can lead to improvements in urban sanitation. This study also highlights the need for further research into the drivers of tool usage.
Groundwater monitoring and specific yield estimation using time-lapse electrical resistivity imaging and machine learning
Authors: Puntu Jordi Mahardika , Chang Ping-Yu , Amania Haiyina Hasbia , Lin Ding-Jiun , Sung Chia-Yu , Suryantara M. Syahdan Akbar , Chang Liang-Cheng , Doyoro Yonatan Garkebo
Published: July 2023

This paper presents an alternative method for monitoring groundwater levels and estimating specific yields of an unconfined aquifer under different seasonal conditions. The approach employs the Time-Lapse Electrical Resistivity Imaging (TL-ERI) method and machine learning-based time series clustering. A TL-ERI survey was conducted at ten sites (WS01-WS10 sites) throughout the dry and wet seasons, with five-time measurements collected for each site, in the Taichung-Nantou Basin along the Wu River, Central Taiwan. The obtained resistivity raw data was inverted and converted into normalized water content values using Archie’s law, followed by applying the Van Genuchten (VG) model for the Soil Water Characteristic Curve to estimate the Groundwater Level (GWL), and estimated the theoretical specific yield (Sy) by computing the difference between the saturated and residual water contents of the fitted VG model. In addition, the specific yield capacity (Sc), representing the nature of the storage capacity in the aquifer, was also calculated. The results showed that this approach was able to estimate those hydrogeological parameters. The spatial distribution of the GWL reveals that during the dry-wet seasons from February to July, there was a high GWL that extended from southeast to northwest. Conversely, during the wet-dry seasons from July to October, the high GWL shrank, which can be attributed to recharge variations from rainfall events. The determined spatial distribution of Sy and Sc fall within the range of 0.03–0.24 and 0.14–0.25, respectively. To quantitatively establish areas of similar groundwater level changes along with the VG model parameter variations during the study period, a Time series Clustering analysis (TSC) was performed by utilizing Hierarchical Agglomerative Clustering (HAC). The findings suggest that the WS03 site is a promising area for further investigation due to its highest Sc value with a slight change in groundwater levels during the dry and wet seasons. This study brings an advanced development of the geoelectrical method to estimate regional hydrogeological parameters in an area with limited available groundwater observation wells, in different seasonal conditions for groundwater management purposes.
Deep learning-based semantic segmentation of remote sensing images: a review
Authors: Lv Jinna , Shen Qi , Lv Mingzheng , Li Yiran , Shi Lei , Zhang Peiying
Published: July 2023

Semantic segmentation is a fundamental but challenging problem of pixel-level remote sensing (RS) data analysis. Semantic segmentation tasks based on aerial and satellite images play an important role in a wide range of applications. Recently, with the successful applications of deep learning (DL) in the computer vision (CV) field, more and more researchers have introduced and improved DL methods to the task of RS data semantic segmentation and achieved excellent results. Although there are a large number of DL methods, there remains a deficiency in the evaluation and advancement of semantic segmentation techniques for RS data. To solve the problem, this paper surveys more than 100 papers in this field in the past 5 years and elaborates in detail on the aspects of technical framework classification discussion, datasets, experimental evaluation, research challenges, and future research directions. Different from several previously published surveys, this paper first focuses on comprehensively summarizing the advantages and disadvantages of techniques and models based on the important and difficult points. This research will help beginners quickly establish research ideas and processes in this field, allowing them to focus on algorithm innovation without paying too much attention to datasets, evaluation indicators, and research frameworks.
Feature selection translates drug response predictors from cell lines to patients
Authors: Yuan Shinsheng , Chen Yen-Chou , Tsai Chi-Hsuan , Chen Huei-Wen , Shieh Grace S.
Published: July 2023

Targeted therapies and chemotherapies are prevalent in cancer treatment. Identification of predictive markers to stratify cancer patients who will respond to these therapies remains challenging because patient drug response data are limited. As large amounts of drug response data have been generated by cell lines, methods to efficiently translate cell-line-trained predictors to human tumors will be useful in clinical practice. Here, we propose versatile feature selection procedures that can be combined with any classifier. For demonstration, we combined the feature selection procedures with a (linear) logit model and a (non-linear) K-nearest neighbor and trained these on cell lines to result in LogitDA and KNNDA, respectively. We show that LogitDA/KNNDA significantly outperforms existing methods, e.g., a logistic model and a deep learning method trained by thousands of genes, in prediction AUC (0.70–1.00 for seven of the ten drugs tested) and is interpretable. This may be due to the fact that sample sizes are often limited in the area of drug response prediction. We further derive a novel adjustment on the prediction cutoff for LogitDA to yield a prediction accuracy of 0.70–0.93 for seven drugs, including erlotinib and cetuximab, whose pathways relevant to anti-cancer therapies are also uncovered. These results indicate that our methods can efficiently translate cell-line-trained predictors into tumors.
Application of single-cell RNA sequencing methods to develop B cell targeted treatments for autoimmunity
Authors: Nicholas Catherine A. , Smith Mia J.
Published: July 2023

The COVID-19 pandemic coincided with several transformative advances in single-cell analysis. These new methods along with decades of research and trials with antibody therapeutics and RNA based technologies allowed for highly effective vaccines and treatments to be produced at astonishing speeds. While these tools were initially focused on models of infection, they also show promise in an autoimmune setting. Self-reactive B cells play important roles as antigen-presenting cells and cytokine and autoantibody producers for many autoimmune diseases. Yet, current therapies to target autoreactive B cells deplete all B cells irrespective of their pathogenicity. Development of self-reactive B cell targeting therapies that would spare non-pathogenic B cells are needed to treat disease while allowing effective immune responses to other ailments. Single-cell RNA sequencing (scRNA-seq) approaches will aid in identification of the pathogenic self-reactive B cells operative in autoimmunity and help with development of more favorable precision targeted therapies.
Effects of dietary Clostridium butyricum on the growth performance, digestion, and intestinal health of spotted sea bass (Lateolabrax maculatus)
Authors: Kong Lumin , Ma Jianrong , Zhou Sishun , Lin Hao , Long Zhongying , Qin Huihui , Liu Longhui , Lin Yi , Huang Zhangfan , Li Zhongbao
Published: July 2023

Clostridium butyricum (CB) is known to promote growth, enhance immunity, promote digestion, and improve intestinal health. In this study, we investigated the effects of CB in the feed on growth performance, digestion, and intestinal health of juvenile spotted sea bass. To provide a theoretical basis for the development and application of CB in the feed of spotted sea bass, a total of 450 spotted sea bass with an initial body weight of (9.58 ± 0.05) g were randomly divided into six groups. Gradient levels with 0, 0.1%, 0.2%, 0.3%, 0.4%, and 0.5% of CB (1×109 cfu/g) were supplemented into diets, designated as CC, CB1, CB2, CB3, CB4, and CB5, respectively. Each group was fed for 54 days. Our results suggest that dietary 0.2% and 0.3% of CB can significantly increase the weight gain (WG) and specific growth rate (SGR) of spotted sea bass. The addition of CB significantly increased intestinal amylase activity, intestinal villus length, intestinal villus width, and intestinal muscle thickness. Similarly, CB supplementation increased the expression of tumor necrosis factor-α (TNF-α) and interleukin-8 (IL-8). Sequence analysis of the bacterial 16S rDNA region showed that dietary CB altered the intestinal microbiota profile of juvenile spotted sea bass, increasing the dominant bacteria in the intestine and decreasing the harmful bacteria. Overall, dietary addition of CB can improve growth performance, enhance intestinal immunity, improve intestinal flora structure, and comprehensively improve the health of spotted sea bass.
Two case reports and a systematic review of the literature on adult cerebral cortical encephalitis with anti-myelin oligodendrocyte glycoprotein antibody
Authors: Xu Meihui , Ma Chi , Dong Ming , Guo Chunjie , Yang Simin , Liu Yue , Wang Xu
Published: July 2023

Background and purpose

Myelin oligodendrocyte glycoprotein antibody-associated disease (MOGAD) has gained recognition in recent years as an immune-mediated inflammatory demyelinating disease of the central nervous system. The clinical features and prognosis of MOGAD adult cerebral cortical encephalitis (adult CCE) have not been fully elucidated. This study aims to further characterize the clinical symptoms, magnetic resonance imaging (MRI) findings, and prognosis of CCE with anti-MOG antibody.

Methods

We present two adult cases of CCE with anti-MOG antibody and summarize the clinical symptoms, magnetic resonance imaging (MRI) findings, and prognosis of this phenotype as per a completed systematic review of the literature.

Results

We found a total of 39 cases of MOGAD adult CCE (36% females; average age of onset of 29 years). Among them, 85% had seizure, 82% had headache, 64% had cortical symptoms, 64% had fever, 54% had changes of consciousness, and 38% had ocular symptoms. All cases demonstrated cerebral cortical T2 fluid-attenuated inversion recovery (FLAIR) lesions on MRI. Of the 25 patients (with seizure or not) who had EEG reports, 76% of patients showed abnormal EEG. Cerebrospinal fluid (CSF) white blood cell count of 90% of patients and CSF total protein of 67% of patients were elevated. In 16 patients with available CSF cytology data, 11 (69%) had abnormal cytology findings with monocytic predominance. In the 15 cases for which MOG antibody IgG was tested in both serum and CSF, 14 (93%) demonstrated a higher positive MOG IgG titer in serum than CSF. The majority of patients were treated with immunosuppressive therapy (97% corticosteroids, 15% mycophenolate mofetil, 13% IVIg, 5% azathioprine, and 5% other). The majority of patients had a favorable prognosis after treatment, as exemplified by improved clinical symptoms and imaging. Two patients relapsed.

Conclusions

The clinical presentation and prognosis of adult CCE remain less understood in comparison to more common MOGAD phenotypes. It is important to consider MOGAD as an underlying etiology for adult CCE, as early detection and immunotherapy may improve outcomes.
Mechanisms and applications of adipose-derived stem cell-extracellular vesicles in the inflammation of wound healing
Authors: Jia Qingyi , Zhao Hanxing , Wang Yixi , Cen Ying , Zhang Zhenyu
Published: July 2023

Wound healing is a sophisticated process consisting of serial phases with overlaps, including hemostasis, inflammation, proliferation, and remodeling. The inflammation response is an early response that plays a crucial role in eliminating microbes and clearing damaged cell debris. However, in some pathological circumstances, such as diabetes mellitus, ischemia, trauma, deep burn, etc., abnormal inflammation can cause impaired wound healing. Adipose-derived stem cells (ADSCs) belong to the mesenchymal stem cell (MSC) family and exhibit prospective applications in tissue regeneration and dermatological repairs. ADSC-secreted extracellular vesicles (ADSC-EVs) mimic the functions of ADSCs without the concerns of cell survival, immune response, or ethical issues. Studies have revealed that ADSC-EVs can inhibit abnormal inflammation responses and accelerate wound healing through various mechanisms. Moreover, some studies explored modifications in the cargo components of ADSC-EVs to enhance their therapeutic efficacy. Given the increasing studies focusing on the potential of ADSC-EVs in wound healing, how they interfere with different phases of this process has been investigated in pieces. In this review, we summarized all up-to-date evidence to map a clearer picture of the underlying mechanisms of ADSC-EVs in inflammation response. The applications of ADSC-EVs aiming at inflammation in the healing process were also reviewed to provide therapeutic strategies for future investigators.
Longitudinal study of humoral immunity against SARS-CoV-2 of health professionals in Brazil: the impact of booster dose and reinfection on antibody dynamics
Authors: Franco-Luiz Ana Paula Moreira , Fernandes Nubia Monteiro Gonçalves Soares , Silva Thais Bárbara de Souza , Bernardes Wilma Patrícia de Oliveira Santos , Westin Mateus Rodrigues , Santos Thais Garcia , Fernandes Gabriel da Rocha , Simões Taynãna César , Silva Eduardo Fernandes E. , Gava Sandra Grossi , Alves Breno Magalhães , de Carvalho Melo Mariana , da Silva-Pereira Rosiane A. , Alves Pedro Augusto , Fonseca Cristina Toscano
Published: July 2023

Introduction

The pandemic caused by SARS-CoV-2 has had a major impact on health systems. Vaccines have been shown to be effective in improving the clinical outcome of COVID-19, but they are not able to fully prevent infection and reinfection, especially that caused by new variants.

Methods

Here, we tracked for 450 days the humoral immune response and reinfection in 52 healthcare workers from Brazil. Infection and reinfection were confirmed by RT-qPCR, while IgM and IgG antibody levels were monitored by rapid test.

Results

Of the 52 participants, 19 (36%) got reinfected during the follow-up period, all presenting mild symptoms. For all participants, IgM levels dropped sharply, with over 47% of them becoming seronegative by the 60th day. For IgG, 90% of the participants became seropositive within the first 30 days of follow-up. IgG antibodies also dropped after this period reaching the lowest level on day 270 (68.5 ± 72.3, p<0.0001). Booster dose and reinfection increased the levels of both antibodies, with the interaction between them resulting in an increase in IgG levels of 130.3 arbitrary units.

Conclusions

Overall, our data indicate that acquired humoral immunity declines over time and suggests that IgM and IgG antibody levels are not associated with the prevention of reinfection.
Cytokine response and damages in the lungs of aging Syrian hamsters on a high-fat diet infected with the SARS-CoV-2 virus
Authors: Fomin Gleb , Tabynov Kairat , Islamov Rinat , Turebekov Nurkeldi , Yessimseit Duman , Yerubaev Toktasyn
Published: July 2023

Hypertriglyceridemia, obesity, and aging are among the key risk factors for severe COVID-19 with acute respiratory distress syndrome (ARDS). One of the main prognostic biomarkers of ARDS is the level of cytokines IL-6 and TNF-α in the blood. In our study, we modeled hyperglyceridemia and hypercholesterolemia on 18-month-old Syrian hamsters (Mesocricetus auratus). By 18 months, the animals showed such markers of aging as weight stabilization with a tendency to reduce it, polycystic liver disease, decreased motor activity, and foci of alopecia. The high-fat diet caused an increase in triglycerides and cholesterol, as well as fatty changes in the liver. On the third day after infection with the SARS-CoV-2 virus, animals showed a decrease in weight in the groups with a high-fat diet. In the lungs of males on both diets, there was an increase in the concentration of IFN-α, as well as IL-6 in both males and females, regardless of the type of diet. At the same time, the levels of TNF-α and IFN-γ did not change in infected animals. Morphological studies of the lungs of hamsters with SARS-CoV-2 showed the presence of a pathological process characteristic of ARDS. These included bronchointerstitial pneumonia and diffuse alveolar damages. These observations suggest that in aging hamsters, the immune response to pro-inflammatory cytokines may be delayed to a later period. Hypertriglyceridemia, age, and gender affect the severity of COVID-19. These results will help to understand the pathogenesis of COVID-19 associated with age, gender, and disorders of fat metabolism in humans.
Circulatory HMGB1 is an early predictive and prognostic biomarker of ARDS and mortality in a swine model of polytrauma
Authors: Young Matthew D. , Cancio Tomas S. , Thorpe Catherine R. , Willis Robert P. , Snook John K. , Jordan Bryan S. , Demons Samandra T. , Salinas Jose , Yang Zhangsheng
Published: July 2023

Acute respiratory distress syndrome (ARDS) is a leading cause of morbidity and mortality in polytrauma patients. Pharmacological treatments of ARDS are lacking, and ARDS patients rely on supportive care. Accurate diagnosis of ARDS is vital for early intervention and improved outcomes but is presently delayed up to days. The use of biomarkers for early identification of ARDS development is a potential solution. Inflammatory mediators high-mobility group box 1 (HMGB1), syndecan-1 (SDC-1), and C3a have been previously proposed as potential biomarkers. For this study, we analyzed these biomarkers in animals undergoing smoke inhalation and 40% total body surface area burns, followed by intensive care for 72 h post-injury (PI) to determine their association with ARDS and mortality. We found that the levels of inflammatory mediators in serum were affected, as well as the degree of HMGB1 and Toll-like receptor 4 (TLR4) signal activation in the lung. The results showed significantly increased HMGB1 expression levels in animals that developed ARDS compared with those that did not. Receiver operating characteristic (ROC) analysis showed that HMGB1 levels at 6 h PI were significantly associated with ARDS development (AUROC=0.77) and mortality (AUROC=0.82). Logistic regression analysis revealed that levels of HMGB1 ≥24.10 ng/ml are associated with a 13-fold higher incidence of ARDS [OR:13.57 (2.76–104.3)], whereas the levels of HMGB1 ≥31.39 ng/ml are associated with a 12-fold increase in mortality [OR: 12.00 (2.36–93.47)]. In addition, we found that mesenchymal stem cell (MSC) therapeutic treatment led to a significant decrease in systemic HMGB1 elevation but failed to block SDC-1 and C3a increases. Immunohistochemistry analyses showed that smoke inhalation and burn injury induced the expression of HMGB1 and TLR4 and stimulated co-localization of HMGB1 and TLR4 in the lung. Interestingly, MSC treatment reduced the presence of HMGB1, TLR4, and the HMGB1-TLR4 co-localization. These results show that serum HMGB1 is a prognostic biomarker for predicting the incidence of ARDS and mortality in swine with smoke inhalation and burn injury. Therapeutically blocking HMGB1 signal activation might be an effective approach for attenuating ARDS development in combat casualties or civilian patients.
Immunomodulatory actions of vitamin D in various immune-related disorders: a comprehensive review
Authors: Ghaseminejad-Raeini Amirhossein , Ghaderi Ali , Sharafi Amirmohammad , Nematollahi-Sani Behrad , Moossavi Maryam , Derakhshani Afshin , Sarab Gholamreza Anani
Published: July 2023

For many years, vitamin D has been acknowledged for its role in maintaining calcium and phosphate balance. However, in recent years, research has assessed its immunomodulatory role and come up with conflicting conclusions. Because the vitamin D receptor is expressed in a variety of immune cell types, study into the precise role of this molecule in diseases, notably autoimmune disorders, has been made possible. The physiologically activated version of vitamin D also promotes a tolerogenic immunological condition in addition to modulating innate and acquired immune cell responses. According to a number of recent studies, this important micronutrient plays a complex role in numerous biochemical pathways in the immune system and disorders that are associated with them. Research in this field is still relatively new, and some studies claim that patients with severe autoimmune illnesses frequently have vitamin D deficiencies or insufficiencies. This review seeks to clarify the most recent research on vitamin D’s immune system-related roles, including the pathophysiology of major disorders.
Modeling the biaxial, rate-dependent response of filament-wound FRP tubes
Authors: Lanning Angela , Zaghi Arash E.
Published: July 2023

This work studies the rate-dependent mechanical behavior of filament-wound fiber-reinforced polymer (FRP) composite pipes. Commercially available tubes with a filament winding angle of ±55° were tested under cyclic axial compression for four loading rates. Stress relaxation under constant strain was observed as well as a dependence of stress on the strain rate. A novel modeling methodology is presented to capture the nonlinear cyclic response, including the viscoelastic behavior of the epoxy matrix and the interaction of axial and hoop strains. This is accomplished by defining an element configuration with separate elements for the epoxy matrix and the glass fibers. The nonlinear and viscoelastic behavior is incorporated using the generalized Maxwell model. A machine learning (ML) calibration framework is adapted for this study and used to calibrate the nonlinear and viscoelastic properties for the analytical model using a convolutional neural network (CNN). The CNN is trained to identify and understand the interdependencies among the model parameters. The calibrated model parameters are used to simulate the experimentally measured response of the FRP tubes and were found to be applicable across the range of strain rates. The proposed modeling methodology accurately predicted the axial stress and hoop strain time histories as well as the rate-dependent stress relaxation during constant axial strains. The accuracy capturing the measured stress-strain responses demonstrated the synthetic dataset was adequate for training the CNN without requiring additional experimental data.
Classification system for nanotechnology-enabled health products with both scientific and regulatory application
Authors: Rodríguez-Gómez Francisco D. , Penon Oriol , Monferrer Dominique , Rivera-Gil Pilar
Published: July 2023

The lack of specific regulatory guidelines for nanotechnology-enabled health products (NHPs) is hampering development and patient access to these innovative technologies. Namely, there is an urgent need for harmonized regulatory definitions and classification systems that allow establishing a standardized framework for NHPs regulatory assessment. In this work, a novel classification system for NHPs is proposed. This classification can be applied for sorting nano-based innovations and regulatory guidelines according to the type of NHPs they address. Said methodology combines scientific and regulatory principles and it is based on the following criteria: principal mode of action, chemical composition, medical purpose and nanomanufacturing approach. This classification system could serve as a useful tool to sensor the state of the art of NHPs which is particularly useful for regulators to support strategy development of regulatory guidelines. Additionally, this tool would also allow manufacturers of NHPs to align their development plans with their applicable guidelines and standards and thus fulfill regulators expectations.
Utility of ACMG classification to support interpretation of molecular genetic test results in patients with factor VII deficiency
Authors: Alesci Rosa Sonja , Hecking Carola , Racké Benjamin , Janssen Detlev , Dempfle Carl-Erik
Published: July 2023

Background

The American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) have introduced an internationally shared framework for variant classification in genetic disorders. FVII deficiency is a rare inherited autosomal recessive bleeding disorder with sparse data concerning ACMG classification.

Methods

To develop an approach which may improve the utility of molecular genetic test results, 129 patients with FVII deficiency were retrospectively assigned to six subgroups for exploratory analysis: F7 gene wildtype (group 1), ACMG 1 (benign variant) or ACMG 2 (likely benign variant), only (group 2), ACMG 3 (variant of uncertain significance) ± ACMG 1–2 heterozygous or not classified variant (group 3), ACMG 4 (likely pathogenic variant), or ACMG 5 (pathogenic variant) single heterozygous ± ACMG 1–3 single heterozygous (group 4), ACMG 4–5 homozygous or ≥2 ACMG 4–5 heterozygous or ≥1 ACMG 4–5 heterozygous plus either ACMG 1 c.1238G>A modifying variant homozygous or ≥2 ACMG 1–3 (group 5), FVII deficiency and another bleeding disorder (group 6).

Results

Eleven of 31 patients (35.5%) in group 5 had abnormal ISTH-BS (n = 7) and/or history of substitution with recombinant factor VIIa (n = 5) versus 4 of 80 patients (5.0%, n = 1 abnormal ISTH-BS, n = 3 substitution) in groups 1 (n = 2/22), 2 (n = 1/29), 3 (n = 0/9), and 4 (n = 1/20). Four of 18 patients (22.2%) with FVII deficiency and another bleeding disorder (group 6) had an abnormal ISTH-BS (n = 2) and/or history of substitution with recombinant factor VIIa (n = 3).

Conclusion

Patients with a homozygous ACMG 4–5 variant or with specific combinations of heterozygous ACMG 4–5 ± ACMG 1–3 variants exhibited a high-risk bleeding phenotype in contrast to the remaining patients without another bleeding disorder. This result may serve as a basis to develop a genotype/phenotype prediction model in future studies.
Pleiotropy drives evolutionary repair of the responsiveness of polarized cell growth to environmental cues
Authors: Kingma Enzo , Diepeveen Eveline T. , Iñigo de la Cruz Leila , Laan Liedewij
Published: July 2023

The ability of cells to translate different extracellular cues into different intracellular responses is vital for their survival in unpredictable environments. In Saccharomyces cerevisiae, cell polarity is modulated in response to environmental signals which allows cells to adopt varying morphologies in different external conditions. The responsiveness of cell polarity to extracellular cues depends on the integration of the molecular network that regulates polarity establishment with networks that signal environmental changes. The coupling of molecular networks often leads to pleiotropic interactions that can make it difficult to determine whether the ability to respond to external signals emerges as an evolutionary response to environmental challenges or as a result of pleiotropic interactions between traits. Here, we study how the propensity of the polarity network of S. cerevisiae to evolve toward a state that is responsive to extracellular cues depends on the complexity of the environment. We show that the deletion of two genes, BEM3 and NRP1, disrupts the ability of the polarity network to respond to cues that signal the onset of the diauxic shift. By combining experimental evolution with whole-genome sequencing, we find that the restoration of the responsiveness to these cues correlates with mutations in genes involved in the sphingolipid synthesis pathway and that these mutations frequently settle in evolving populations irrespective of the complexity of the selective environment. We conclude that pleiotropic interactions make a significant contribution to the evolution of networks that are responsive to extracellular cues.
Iron or sulfur respiration—an adaptive choice determining the fitness of a natronophilic bacterium Dethiobacter alkaliphilus in geochemically contrasting environments
Authors: Zavarzina Daria G. , Merkel Alexander Yu , Klyukina Alexandra A. , Elizarov Ivan M. , Pikhtereva Valeria A. , Rusakov Vyacheslav S. , Chistyakova Nataliya I. , Ziganshin Rustam H. , Maslov Alexey A. , Gavrilov Sergey N.
Published: July 2023

Haloalkaliphilic microorganisms are double extremophiles functioning optimally at high salinity and pH. Their typical habitats are soda lakes, geologically ancient yet widespread ecosystems supposed to harbor relict microbial communities. We compared metabolic features and their determinants in two strains of the natronophilic species Dethiobacter alkaliphilus, the only cultured representative of the class “Dethiobacteria” (Bacillota). The strains of D. alkaliphilus were previously isolated from geographically remote Mongolian and Kenyan soda lakes. The type strain AHT1T was described as a facultative chemolithoautotrophic sulfidogen reducing or disproportionating sulfur or thiosulfate, while strain Z-1002 was isolated as a chemolithoautotrophic iron reducer. Here, we uncovered the iron reducing ability of strain AHT1T and the ability of strain Z-1002 for thiosulfate reduction and anaerobic Fe(II) oxidation. Key catabolic processes sustaining the growth of both D. alkaliphilus strains appeared to fit the geochemical settings of two contrasting natural alkaline environments, sulfur-enriched soda lakes and iron-enriched serpentinites. This hypothesis was supported by a meta-analysis of Dethiobacterial genomes and by the enrichment of a novel phylotype from a subsurface alkaline aquifer under Fe(III)-reducing conditions. Genome analysis revealed multiheme c-type cytochromes to be the most probable determinants of iron and sulfur redox transformations in D. alkaliphilus. Phylogeny reconstruction showed that all the respiratory processes in this organism are likely provided by evolutionarily related early forms of unconventional octaheme tetrathionate and sulfite reductases and their structural analogs, OmhA/OcwA Fe(III)-reductases. Several phylogenetically related determinants of anaerobic Fe(II) oxidation were identified in the Z-1002 genome, and the oxidation process was experimentally demonstrated. Proteomic profiling revealed two distinct sets of multiheme cytochromes upregulated in iron(III)- or thiosulfate-respiring cells and the cytochromes peculiar for Fe(II) oxidizing cells. We suggest that maintaining high variation in multiheme cytochromes is an effective adaptive strategy to occupy geochemically contrasting alkaline environments. We propose that sulfur-enriched soda lakes could be secondary habitats for D. alkaliphilus compared to Fe-rich serpentinites, and that the ongoing evolution of Dethiobacterales could retrace the evolutionary path that may have occurred in prokaryotes at a turning point in the biosphere’s history, when the intensification of the sulfur cycle outweighed the global significance of the iron cycle.
The waterbodies of the halo-volcanic Dallol complex: earth analogs to guide us, where to look for life in the universe
Authors: Moors Hugo , De Craen Mieke , Smolders Carla , Provoost Ann , Leys Natalie
Published: July 2023

Microbes are the Earth life forms that have the highest degree of adaptability to survive, live, or even proliferate in very hostile environments. It is even stated that microbes can cope with any extreme physico-chemical condition and are, therefore, omnipresent all over the Earth: on all the continents, inside its crust and in all its waterbodies. However, our study suggests that there exists areas and even water rich environments on Earth where no life is possible. To support the fact that water rich environments can be lifeless, we performed an extensive survey of 10 different hyper extreme waterbodies of the halo-volcanic Dallol complex (Danakil depression, Ethiopia, Horn of Africa). In our study, we combined physico-chemical analyses, mineralogical investigations, XRD and SEM–EDX analyses, ATP measurements, 16S rDNA microbial community determinations, and microbial culturing techniques. According to our findings, we suggest that the individual physico-chemical parameters, water activity, and kosmo-chaotropicity, are the two most important factors that determine whether an environment is lifeless or capable of hosting specific extreme lifeforms. Besides, waterbodies that contained saturated levels of sodium chloride but at the same time possessed extreme low pH values, appeared to be poly-extreme environments in which no life could be detected. However, we clearly discovered a low diversity microbial community in waterbodies that were fully saturated with sodium chloride and only mildly acidic. Our results can be beneficial to more precisely classify whole or certain areas of planetary bodies, including water rich environments, as either potentially habitable or factual uninhabitable environments.
First report of GI.1aP-GI.2 recombinants of rabbit hemorrhagic disease virus in domestic rabbits in China
Authors: Li Yan , Du Deyan , Zhou Long , Su Liyin , You Chengcheng , Zhang Huai , Yu Jifeng , Xiao Lu , Huang Jian
Published: July 2023

The rabbit hemorrhagic disease virus 2 (RHDV2 or GI.2) is a highly contagious agent leading to lethal disease in rabbits. It frequently recombines with other Lagovirus genus, generating epidemical variants with high pathogenicity. In this study, twenty-two liver samples tested positive for GI.2 VP60 gene, were collected in rabbit farms from several geographical regions in China. All GI.2 positive specimens were submitted for RT-PCR detection, nucleotide sequencing and phylogenetic analysis. In addition, suspected GI.2 recombinants were evaluated for virus virulence. The results showed that nine presumptive recombinants were identified by testing for RdRp-VP60 recombination. In these recombinants, four were selected to fully characterize the genome of novel GI.2 recombinant variants, which were described as GI.1aP-GI.2. The nucleotide sequence of these novel variants showed unique recombination pattern and phylogenetic features compared to currently prevalent GI.2 variants. Furthermore, this distinctive recombination of new variant SCNJ-2021 moderately enhanced the virulence of GI.2, even for rabbits vaccinated against parental GI.2. In conclusion, the novel GI.1aP-GI.2 recombinants were identified in rabbit industry in China for the first time, which expanded the knowledge on the phylodynamics and genomic diversity of GI.2 genotype. The rapid molecular evolution and varied pathogenicity of these virus recombinants highlight the urgent need for epidemiological surveillance and for future prevention of these neglected GI.2 variants.
Role of microbial electrosynthesis system in CO2 capture and conversion: a recent advancement toward cathode development
Authors: Ibrahim Irwan , Salehmin Mohd Nur Ikhmal , Balachandran Krishan , Hil Me Muhammad Farhan , Loh Kee Shyuan , Abu Bakar Mimi Hani , Jong Bor Chyan , Lim Swee Su
Published: July 2023

Microbial electrosynthesis (MES) is an emerging electrochemical technology currently being researched as a CO2 sequestration method to address climate change. MES can convert CO2 from pollution or waste materials into various carbon compounds with low energy requirements using electrogenic microbes as biocatalysts. However, the critical component in this technology, the cathode, still needs to perform more effectively than other conventional CO2 reduction methods because of poor selectivity, complex metabolism pathways of microbes, and high material cost. These characteristics lead to the weak interactions of microbes and cathode electrocatalytic activities. These approaches range from cathode modification using conventional engineering approaches to new fabrication methods. Aside from cathode development, the operating procedure also plays a critical function and strategy to optimize electrosynthesis production in reducing operating costs, such as hybridization and integration of MES. If this technology could be realized, it would offer a new way to utilize excess CO2 from industries and generate profitable commodities in the future to replace fossil fuel-derived products. In recent years, several potential approaches have been tested and studied to boost the capabilities of CO2-reducing bio-cathodes regarding surface morphology, current density, and biocompatibility, which would be further elaborated. This compilation aims to showcase that the achievements of MES have significantly improved and the future direction this is going with some recommendations.

Highlights

– MES approach in carbon sequestration using the biotic component.

– The role of microbes as biocatalysts in MES and their metabolic pathways are discussed.

– Methods and materials used to modify biocathode for enhancing CO2 reduction are presented.
Long-term effects of chloropicrin fumigation on soil microbe recovery and growth promotion of Panax notoginseng
Authors: Wang Xin , Wang Qing , Li Wenjing , Zhang Daqi , Fang Wensheng , Li Yuan , Wang Qiuxia , Cao Aocheng , Yan Dongdong
Published: July 2023

Introduction

Panax notoginseng is a precious Chinese medicinal material. Soil fumigation can control soil-borne disease and overcome the continuous cropping obstacles of P. notoginseng. However, chloropicrin (CP) fumigation can kill non-target soil microorganisms and reduce microbial diversity, but the long-time impacts of CP fumigation on soil microbial are less reported.

Methods

We studied the long-term effects of CP fumigation on soil microbes with high-throughput gene sequencing, and correlated the changes in the composition of microbial communities with environmental factors like soil physicochemical properties and soil enzyme activities. This study mainly focuses on the recovery characteristics of soil microbe after soil fumigation by evaluating the ecological restoration of P. notoginseng soil, its sustained control effect on plant diseases, and its promotion effect on crop growth by focusing on the CP fumigation treatment.

Results

The results showed that CP fumigation significantly increased soil available phosphorus (P) to 34.6 ~ 101.6 mg/kg and electrical conductivity (EC) by 18.7% ~ 34.1%, respectively. High-throughput gene sequencing showed that soil fumigation with CP altered the relative abundance of Trichoderma, Chaetomium, Proteobacteria, and Chloroflexi in the soil while inhibiting a lot of Fusarium and Phytophthora. The inhibition rate of Phytophthora spp. was still 75.0% in the third year after fumigation. Fumigation with CP enhanced P. notoginseng’s survival rate and stimulated plant growth, ensuring P. notoginseng’s healthy in the growth period. The impact of fumigation on microbial community assembly and changes in microbial ecological niches were characterized using normalized stochasticity ratio (NST) and Levins’ niche breadth index. Stochasticity dominated bacterial community assembly, while the fungal community was initially dominated by stochasticity and later by determinism. Fumigation with CP reduced the ecological niches of both fungi and bacteria.

Conclusion

In summary, the decrease in microbial diversity and niche caused by CP fumigation could be recovered over time, and the control of soil pathogens by CP fumigation remained sustainable. Moreover, CP fumigation could overcome continuous cropping obstacles of P. notoginseng and promote the healthy growth of P. notoginseng.
Embryonic perfect repair inspired electrospun nanofibers dressing with temperature-sensitive and antibacterial properties for wound healing
Authors: Qi Qinbing , Li Rongkai , Wang Chunhua , Hou Guige , Li Chengbo
Published: July 2023

Introduction

The development of highly effective wound dressings is crucial for successful clinical applications. Achieving wound closure, preventing infection, and minimizing scarring are key objectives in wound healing. Drawing inspiration from the regenerative mechanisms observed in embryonic tissue repair, we designed a series of wound-contractible dressings with exceptional antibacterial properties.

Methods

This was achieved by encapsulating quaternized silicone (QP12) and poly(N-isopropylacrylamide-co-N-hydroxymethylacrylamide-co-octadecyl acrylate) (PNNS) within electrospun nanofibers of poly(ε-caprolactone) (PCL).

Results and discussion

The resulting nanofibrous dressings demonstrated remarkable thermo-responsive self-contraction and tissue adhesion capabilities, enabling secure adherence to the skin and active wound closure. Notably, these nanofibers exhibited potent antibacterial activity against both Gram-positive and Gram-negative bacteria. Furthermore, they possessed desirable properties such as hydrophilicity, biocompatibility and mechanical properties resembling human skin. A full-thickness skin defect model evaluation revealed that these temperature-sensitive nanofibers expedited wound closure, enhanced wound healing, and suppressed scar formation. This result was evidenced by reduced infiltration of inflammatory cells, well-organized collagen arrangement, and improved vascularization. In summary, we propose that these wound-contractible nanofibers, with their antibacterial and anti-scarring properties, hold great promise as an advanced solution for skin wound repair.
Association between superior longitudinal fasciculus, motor recovery, and motor outcome after stroke: a cohort study
Authors: Jacquemont Thomas , Valabregue Romain , Daghsen Lina , Moulton Eric , Zavanone Chiara , Lamy Jean Charles , Rosso Charlotte
Published: July 2023

Introduction

Parieto-frontal interactions are mediated by the superior longitudinal fasciculus (SLF) and are crucial to integrate visuomotor information and mediate fine motor control. In this study, we aimed to characterize the relation of white matter integrity of both parts of the SLF (SLF I and SLF II) to both motor outcome and recovery and its evolution over time in stroke patients with upper limb motor deficits.

Materials and methods

Fractional anisotropy (FA) values over the SLF I, SLF II, and corticospinal tract (CST) and upper limb motor performance evaluated by both the upper limb Fugl-Meyer Assessment score and maximum grip strength were measured for 16 patients at 3 weeks, 6 weeks, and 12 weeks poststroke. FA changes were assessed over time using repeated-measures Friedman ANOVA, and correlations between motor recovery, motor outcome at 12 weeks, and FA values in the CST, SLF I, and SLF II at 3 weeks were performed using Spearman's rank-order correlation.

Results

FA values in the affected hemisphere's SLF I and SLF II at 3 weeks correlated with motor recovery at 12 weeks when assessed by the Fugl-Meyer Assessment for upper limb extremity (rho: 0.502, p: 0.04 and rho: 0.510, p: 0.04, respectively) but not when assessed by grip strength. FA values in the SLF I and SLF II were not correlated with motor outcomes. FA values in the SLF II in the affected hemisphere changed significantly over time (p: 0.016).

Conclusion

Both SLF I and SLF II appeared to participate in poststroke motor recovery of complex movements but not in the motor outcome. These results argue that visually/spatially oriented motor tasks as well as more complex motor tasks using parietal associative areas should be used for poststroke rehabilitation strategies.
Prediction model for long-term seizure and developmental outcomes among children with infantile epileptic spasms syndrome
Authors: Arai Yuto , Okanishi Tohru , Kanai Sotaro , Nakamura Yuko , Sunada Hiroshi , Murakami Hinata , Yamauchi Kazuki , Noma Hisashi , Maegaki Yoshihiro
Published: July 2023

Introduction

Children with infantile epileptic spasms syndrome (IESS) are likely to experience poor outcomes. Researchers have investigated the factors related to its long-term prognosis; however, none of them developed a predictive model.

Objective

This study aimed to clarify the factors that influence the long-term prognosis of seizures and their development and to create a prediction model for IESS.

Materials and methods

We conducted a retrospective cohort study enrolling participants diagnosed with IESS at the Tottori University Hospital. We examined the seizure and developmental status at 3 and 7 years after the IESS onset and divided the participants into favorable and poor outcome groups. Subsequently, we analyzed the factors associated with the poor outcome group and developed a prediction model at 3 years by setting cutoff values using the receiver operating characteristic curve.

Results

Data were obtained from 44 patients with IESS (19 female patients and 25 male patients). Three years after epileptic spasms (ES) onset, seizure and development were the poor outcomes in 15 (34.9%) and 27 (61.4%) patients, respectively. The persistence of ES or tonic seizures (TS) after 90 days of onset, moderate or severe magnetic resonance imaging abnormalities, and developmental delay before IESS onset were significantly associated with poor outcomes. Seven years after the onset of ES, seizures and development were the poor outcomes in 9 (45.0%) and 13 (72.2%) patients, respectively. We found that no factor was significantly associated with poor seizure outcomes, and only developmental delay before IESS onset was significantly associated with poor developmental outcomes. Our prediction model demonstrated 86.7% sensitivity and 64.3% specificity for predicting poor seizure outcomes and 88.9% sensitivity and 100% specificity for predicting poor developmental outcomes.

Conclusion

Our prediction model may be useful for predicting the long-term prognosis of seizures and their development after 3 years. Understanding the long-term prognosis during the initial treatment may facilitate the selection of appropriate treatment.