bluuebunny/crossref_metadata_2025 huggingface dataset:
Changes in the acoustically evoked activity in the inferior colliculus of the rat after functional ablation of the auditory cortex
Authors: Nwabueze-Ogbo FC , Popelář J , Syka J
Published: February 2024

The role of the cortico-tectal pathways in the processing of auditory signals was investigated by recording the click-evoked responses and extracellular multiple unit activity in the inferior colliculus (IC) after functional ablation of the auditory cortex (AC) by local intracortical application of a sodium channel blocker, tetrodotoxin (TTX). Click-evoked IC responses (IC-ER) and multiple unit activity in response to tone bursts were recorded with implanted electrodes in the IC of rats lightly anaesthetized with xylazine. Neural activity was recorded before and after the application of TTX into the ipsilateral auditory cortex (AC) through three implanted cannulas in a total dose of 30 ng. The functional status of the AC was monitored by recording click-evoked middle latency responses from a ball electrode implanted on the AC. During inactivation of the AC, IC-ER amplitudes were either increased (48 % of the cases), decreased (32 % of the cases) or not evidently changed (20 % of the cases). Corresponding effects were observed in the firing rate of IC neurons. Functional ablation of the AC also resulted in a significant prolongation of the latencies of individual waves of the IC-ER. However, the discharge pattern of the multiple unit responses, response thresholds and tuning were not altered during AC inactivation. IC neural activity recovered within several hours, and maximally during 2 days. The results reveal principles of the interaction of cortico-tectal pathways with IC neuronal activity.
‘Take your unseen heart and make it into art’: Aesthetic Transformation and Emotional Democracy
Authors: Früchtl Josef
Published: February 2024

This article wants to answer three questions: first, why is not only sensibility but visibility important for modern democracy? Second, why is art or aesthetic experience important for both democracy and visibility? And third, how is it possible that aesthetic experience generates effects that conduce to democracy? Answering these questions aims at highlighting an inner connection between democracy, feelings and aesthetics. For a democratic community, on the one hand, cannot exclude feelings from political discourse, but, on the other hand, cannot accept them in their immediate and absolute form. Feelings need ‘transformation’, and the best popular medium for this is aesthetic experience.
Axial Compressor as eBooster for charging an Ultra-Lean-Burn Hydrogen Combustion Engine
Authors:   Leibniz Universität Hannover, Schulz Yannik , Seume Joerg R. ,   Leibniz Universität Hannover, Sagan Lukas ,   Technische Universität Braunschweig, Eilts Peter ,   Technische Universität Braunschweig
Published: February 2024

Hydrogen as a fuel in spark-ignition combustion engines provides an opportunity for using an ultra-lean-burn combustion strategy. This combustion concept has the advantage of ensuring a high thermal efficiency as well as ultra-low NOx emissions at the same time. This makes it an interesting concept, especially in the field of commercial vehicles. Providing these high pressure ratios while guaranteeing an acceptable boost pressure is challenging for charging systems. In order to face these requirements, an axial compressor eBooster stage is developed. The eBooster concept extends the operating range of a single-stage turbocharger. Otherwise, a complex and cost intensive two-stage configuration would be needed. The compressor is designed to operate for mass flow rates of 0.4 to 0.8 kg/s and total pressure ratios of up to 1.72. When operating the eBooster stage, the centrifugal compressor performance map is shifted towards higher mass flow rates by means of pre-compression. The compressor developed shows a peak isentropic efficiency of 82.8 % with high efficiencies (>78 %) for the whole operating range.
Modelling individual plants’ growth: competition of Viola arvensis and wheat
Authors: von Redwitz Christoph , Lepke Janin , Richter Otto
Published: February 2024

Introduction

Competition by weeds is a severe threat to agricultural crops. While these days the broadcast of herbicides over the entire field is common praxis, new technologies promise to reduce chemical output by reducing the area sprayed. The maximum precision would be a single plant treatment. This precision will allow a single plant management, which requires single plant management decisions, which is far beyond the possibilities of current praxis. A plant specific management decision can only be made on the basis of a model simulation.

Materials and methods

A simulation model was developed to evaluate the effect of spatially explicit weed management covering interaction between single plants. The governing equations consist of coupled nonlinear differential equations for growth and competition of crop and weed plants in a spatial setting i.e. a coordinate is assigned to each plant. The mutual interaction is determined by the parameters strength and range of competition. Furthermore, an experiment was carried out parallel to the development of the model involving wheat and Viola arvensis (Murr.), in which coordinates and growth curves for a large number of plants (~600) were recorded allowing for a reasonable parameterization of the model.

Results and discussion

The model is able to evaluate spatially explicit management measures such as weed strip control based on the height growth of single plants. The model is capable of evaluating a variety of control measures such as the frequency and spatial allocation of treatments. In particular, the effect of the width of a treatment zone around the rows of the crop was simulated.

Conclusion

In future, the developed model could be extended to a decision support system for single plant weed management. Making decisions plant-by-plant, allows to orchestrate the weed management in a way that takes into account competing goals in plant protection: yield and biodiversity.
Study on the mechanism of MDSC-platelets and their role in the breast cancer microenvironment
Authors: Han Xinpu , Song Xiaotong , Xiao Zhigang , Zhu Guanghui , Gao Ruike , Ni Baoyi , Li Jie
Published: February 2024

Myeloid-derived suppressor cells (MDSCs) are key immunosuppressive cells in the tumor microenvironment (TME) that play critical roles in promoting tumor growth and metastasis. Tumor-associated platelets (TAPs) help cancer cells evade the immune system and promote metastasis. In this paper, we describe the interaction between MDSCs and TAPs, including their generation, secretion, activation, and recruitment, as well as the effects of MDSCs and platelets on the generation and changes in the immune, metabolic, and angiogenic breast cancer (BC) microenvironments. In addition, we summarize preclinical and clinical studies, traditional Chinese medicine (TCM) therapeutic approaches, and new technologies related to targeting and preventing MDSCs from interacting with TAPs to modulate the BC TME, discuss the potential mechanisms, and provide perspectives for future development. The therapeutic strategies discussed in this review may have implications in promoting the normalization of the BC TME, reducing primary tumor growth and distant lung metastasis, and improving the efficiency of anti-tumor therapy, thereby improving the overall survival (OS) and progression-free survival (PFS) of patients. However, despite the significant advances in understanding these mechanisms and therapeutic strategies, the complexity and heterogeneity of MDSCs and side effects of antiplatelet agents remain challenging. This requires further investigation in future prospective cohort studies.
A thermodynamic comparison of membrane-assisted processes for hydrogen production with integrated CO2 capture
Authors: Pouw S. , Bevers M. , Gallucci F. , Van Sint Annaland M.
Published: February 2024

The energy efficiency of two novel process designs for the production of ultra-pure hydrogen with simultaneous capture of CO2 using CH4 as the feedstock, namely membrane-assisted chemical looping reforming (MA-CLR) and membrane-assisted sorption-enhanced reforming (MA-SER) has been compared. The modelling of the integrated network for mass and heat balances has been carried out using the ASPEN® Plus V10 process simulation tool to quantify the benefits and disadvantages of integrating hydrogen perm-selective membranes with either chemical looping or sorption-enhanced reforming. The evaluation of the MA-CLR process is carried out for a range of the following operating conditions: 10 < pR < 60 bar, 500 < TR < 900°C, and 1.5 < H2O/CH4 < 3.0. On the other hand, for the MA-SER process the operation ranges of 1.0 < pR < 10 bar, 400 < TR < 900°C, and 2.5 < H2O/CH4 < 4.0 were considered. Within the operation window of the MA-SER process, no carbon formation is observed, as any carbon present in the system reacts with CaO in the form of CO2. However, in the case of the MA-CLR process, carbon formation can occur during the pre-reforming stage, particularly at low H2O/CH4 ratios. In terms of hydrogen yield, energy utilization and carbon capture, the MA-CLR outperforms the MA-SER plant. However, the MA-SER plant offers certain advantages over the MA-CLR system, such as a pure CO2 product stream and lower reactor design temperatures. In the MA-CLR system, a carbon capture rate of 99.8% and a hydrogen product yield of 74.4% are achieved, whereas the MA-SER plant achieves a carbon capture rate of 98.5% and a hydrogen product yield of 69.7%.
Bacteroidaceae, Bacteroides, and Veillonella: emerging protectors against Graves’ disease
Authors: Liu Siyuan , Li Fan , Cai Yunjia , Ren Linan , Sun Lin , Gang Xiaokun , Wang Guixia
Published: February 2024

Background

Graves’ disease (GD) is the most common cause of hyperthyroidism, and its pathogenesis remains incompletely elucidated. Numerous studies have implicated the gut microbiota in the development of thyroid disorders. This study employs Mendelian randomization analysis to investigate the characteristics of gut microbiota in GD patients, aiming to offer novel insights into the etiology and treatment of Graves’ disease.

Methods

Two-sample Mendelian randomization (MR) analysis was employed to assess the causal relationship between Graves’ disease and the gut microbiota composition. Gut microbiota data were sourced from the international consortium MiBioGen, while Graves’ disease data were obtained from FINNGEN. Eligible single nucleotide polymorphisms (SNPs) were selected as instrumental variables. Multiple analysis methods, including inverse variance-weighted (IVW), MR-Egger regression, weighted median, weighted mode, and MR-RAPS, were utilized. Sensitivity analyses were conducted employing MR-Egger intercept test, Cochran’s Q test, and leave-one-out analysis as quality control measures.

Results

The Mendelian randomization study conducted in a European population revealed a decreased risk of Graves’ disease associated with Bacteroidaceae (Odds ratio (OR) [95% confidence interval (CI)]: 0.89 [0.89 ~ 0.90], adjusted P value: <0.001), Bacteroides (OR: [95% CI]: 0.555 [0.437 ~ 0.706], adjusted P value: <0.001), and Veillonella (OR [95% CI]: 0.632 [0.492 ~ 0.811], adjusted P value: 0.016). No significant evidence of heterogeneity, or horizontal pleiotropy was detected. Furthermore, the preliminary MR analysis identified 13 bacterial species including Eubacterium brachy group and Family XIII AD3011 group, exhibiting significant associations with Graves’ disease onset, suggesting potential causal effects.

Conclusion

A causal relationship exists between gut microbiota and Graves’ disease. Bacteroidaceae, Bacteroides, and Veillonella emerge as protective factors against Graves’ disease development. Prospective probiotic supplementation may offer a novel avenue for adjunctive treatment in the management of Graves’ disease in the future.
Stakeholder-driven carbon neutral pathways for Thailand and Bangkok: integrated assessment modeling to inform multilevel climate governance
Authors: Waite Taryn , Pradhan Bijay Bahadur , Winyuchakrit Pornphimol , Khan Zarrar , Weber Maridee , Pressburger Leeya , Chaichaloempreecha Achiraya , Rajbhandari Salony , Pita Piti , Westphal Michael I. , Jonvisait Abdullah , Jareemit Daranee , Limmeechokchai Bundit , Evans Meredydd
Published: February 2024

Thailand has established a target of carbon neutrality by 2050. Reaching this goal will require coordination and collaboration between stakeholders spanning sectors and scales, including energy system decision makers, land managers, and city planners. Robust decarbonization scenarios incorporating current plans and targets, additional measures needed, and trade-offs between strategies can help stakeholders make informed decisions in the face of uncertainty. Through iterative engagement with decision makers at the city and national levels, we develop and analyze carbon neutral scenarios for Thailand that incorporate Bangkok’s role using a global integrated assessment model. We find that Thailand can reach carbon neutrality through power sector decarbonization, energy efficiency improvements, widespread electrification, and advanced technologies including carbon capture and storage and hydrogen. Negative emissions technologies will also be needed to offset Thailand and Bangkok’s hardest-to-abate CO2 emissions. Bangkok, as a major population and economic center, contributes significantly to Thailand’s energy demand and emissions and can therefore play an important role in climate change mitigation. Accordingly, our results underscore the importance of subnational climate action in meeting Thailand’s carbon neutral goal. Our analysis also indicates that without sustained land-based carbon sequestration, much more mitigation effort will be needed in Thailand’s energy sector, including at the subnational scale, to reach carbon neutrality. These insights can help stakeholders identify priorities, consider tradeoffs, and make decisions that will impact Bangkok and Thailand’s long-term climate change mitigation potential. This analysis demonstrates how stakeholder engagement in integrated assessment modeling can facilitate and inform multilevel climate governance.
Motion behavior of a high-current fault electric arc occurred in the dead zone of protection in a substation
Authors: Teng Jun , Zhang Yongjie , Chen Danhua , Sheng Ji , Wang Shuaijie , Huang Wei
Published: February 2024

Since the dead-zone fault in substations often has a relatively long removal time, it may damage the insulation of power equipment and even threaten the stability of the power system. In this paper, the movement of the dead-zone fault electric arc in a 220-kV substation is investigated. The arc chain model for the dead-zone fault electric arc is developed; the influences of electromagnetic force, thermal buoyancy, and the air resistance stressed on the electric arc are comprehensively considered. The electric arc velocity and displacement are computed. Then, the spreading characteristics of the dead-zone electric arc under various conditions are studied. The spreading trend of the dead-zone fault electric arc is summarized. Finally, measures to inhibit the spreading of the electric arc are suggested. The study indicates that the movement of the electric arc in the dead zone during the early stage is primarily influenced by the electromagnetic force resulting from the overpass and conductor, and the arc is concave and has an irregular trajectory. The inclination angle of the conductor significantly affects the direction of the electromagnetic force. If the conductor is laid horizontally, the electric arc is subjected to a smaller force. The electromagnetic force stressed on the electric arc is mainly attributed to the fault phase conductor and the electric arc body itself, whereas those from the other phase conductors are minor. The initial position of the arc root has a certain impact on the movement of the electric arc. The use of the insulating materials restricts the arc root movement.
Study on the impact of regional carbon emissions on enterprise technological innovation under the background of low-carbon transformation in China
Authors: Lu Hualiang , Xie Zhenying , Liu Yongchun , Xu Guangwei
Published: February 2024

Low-carbon transition, as the backbone of corporate innovation drive, has an important strategic position globally. In order to avoid heterogeneous intercepts related to explanatory variables or interfering with each other, this paper empirically examines the impact of regional carbon emissions on corporate technological innovation and its mechanism based on the data of listed companies in China from 2009 to 2020, using a fixed-effects model. It is found that 1) the reduction of regional carbon emissions is favourable to corporate technological innovation; 2) in terms of the impact mechanism, the reduction of regional carbon emissions promotes corporate technological innovation by enhancing R&D investment and reducing financing constraints. 3) Based on the study of heterogeneity, it is found that: from the perspective of spatial distribution, regional carbon emissions show the phenomenon of “high on both sides and low in the middle”; state-owned enterprises refer to wholly state-owned enterprises, wholly state-owned companies and state-owned capital holding companies in which the State Council and the local people’s governments respectively perform the responsibilities of funders on behalf of the state. In terms of the nature of equity, compared with state-owned enterprises, regional carbon emissions have a greater impact on the technological innovation of non-state-owned enterprises. 4) Further analysis reveals that the low-carbon city pilot policy is conducive to regional carbon emission reduction. Through the comparison before and after the implementation of low carbon policy, this paper reliably verifies that the introduction of urban carpet policy is conducive to regional carbon emissions, and explores the issue of enterprise technological innovation from the perspective of low carbon transformation, providing theoretical support for the carbon emission reduction efforts and the improvement of the technological innovation capacity of different enterprises. At the same time, it fully affirmed the important role of regional carbon emissions, continued to deepen the process of green transformation of enterprises, and boosted the high-quality development of low-carbon enterprises.
Assessing microbial diversity in Yellowstone National Park hot springs using a field deployable automated nucleic acid extraction system
Authors: Wood Jason M. , Urbaniak Camilla , Parker Ceth , Singh Nitin Kumar , Wong Season , Arumugam Arunkumar , Skorupa Dana J. , Hemmah Ashlyn , Laaguiby Phoebe , Karouia Fathi , Peyton Brent M. , Tighe Scott , Venkateswaran Kasthuri
Published: February 2024

Microbial diversity estimation involves extracting nucleic acids from intricate sample matrices. Preparing nucleic acid samples is time-consuming, necessitating effective cell lysis and obtaining pure, inhibitor-free nucleic acid purifications before further use. An automated system offers advantages for field deployment due to its ease of use and quick autonomous results. This is especially beneficial for rapid measurement of in situ microbial diversity in remote areas. Our study aimed to assess microbial diversity of Yellowstone hot springs using a field-deployable lab in a resource-limited remote setting and demonstrate on-site nucleic acid sample processing and sequencing. We collected microbial mat and sediment samples from several Yellowstone National Park hot springs, focusing on the Five Sister Springs (FSS), spring LNN010, and Octopus Spring (OS). The samples were processed for DNA extraction on-site and further sequenced in the lab for microbial diversity. In addition, DNA extracted from one sample was sequenced and analyzed on-site as proof-of-concept. Using either Illumina or Oxford Nanopore Technology sequencing, we found similar microbial diversities. Bacteria (over 90%) were predominant at the FSS and OS sites, with archaea accounting for less than 10%. Metagenomic results were taxonomically categorized based on the closest known organism with a sequenced genome. The dominant archaeal community member was Candidatus Caldiarchaeum subterraneum, and among bacteria, Roseiflexus sp. RS-1 was abundant in mat samples. Interestingly, Bacterium HR17 was also frequently found, suggesting the need for more research on this newly recognized bacterial community member. The presence of Bacterium HR17 in these hot springs suggests its potential role in nitrogen cycling, informing both ecological understanding and industrial potential. This pioneering study assessed the microbiome of Yellowstone hot springs in about 8-9 hours using an automated system for nucleic acid extraction. By its deployment, the system’s value in elucidating the microbial diversity of extreme environments without the need to bring samples to the lab for processing had been highlighted. Sample processing and sequencing had been included in the benefits of the field-deployable lab, and the Nanopore platform had been utilized.
Neutralizing antibody levels detected early after mRNA-based vaccination do not predict by themselves subsequent breakthrough infections of SARS-CoV-2
Authors: Alonso Roberto , Gil-Manso Sergio , Catalán Pilar , Sánchez-Arcilla Ignacio , Marzola Marco , Correa-Rocha Rafael , Muñoz Patricia , Pion Marjorie ,   the Gregorio Marañón Microbiology-ID COVID-19 Study Group
Published: February 2024

The development of mRNA vaccines represented a significant achievement in response to the global health crisis during the SARS-CoV-2 pandemic. Evaluating vaccine efficacy entails identifying different anti-SARS-CoV-2 antibodies, such as total antibodies against the Receptor Binding Domain (RBD) of the S-protein, or neutralizing antibodies (NAbs). This study utilized an innovative PETIA-based kit to measure NAb, and the investigation aimed to assess whether levels of anti-RBD IgG and NAb uniformly measured 30 days after vaccination could predict individuals at a higher risk of subsequent infection in the months following vaccination. Among a cohort of healthy vaccinated healthcare workers larger than 6,000, 12 mRNA-1273- and 115 BNT162b2-vaccinated individuals contracted infections after the first two doses. The main finding is that neither anti-RBD IgG nor NAb levels measured at day 30 post-vaccination can be used as predictors of breakthrough infections (BI). Therefore, the levels of anti-SARS-CoV-2 antibodies detected shortly after vaccination are not the pivotal factors involved in antiviral protection, and other characteristics must be considered in understanding protection against infection. Furthermore, the levels of anti-RBD and NAbs followed a very similar pattern, with a correlation coefficient of r = 0.96. This robust correlation would justify ceasing the quantification of NAbs, as the information provided by both determinations is highly similar. This optimization would help allocate resources more efficiently and speed up the determination of individuals’ humoral immunity status.
Identification of conserved cross-species B-cell linear epitopes in human malaria: a subtractive proteomics and immuno-informatics approach targeting merozoite stage proteins
Authors: Musundi Sebastian D. , Gitaka Jesse , Kanoi Bernard N.
Published: February 2024

Human malaria, caused by five Plasmodium species (P. falciparum, P. vivax, P. malariae, P. ovale, and P. knowlesi), remains a significant global health burden. While most interventions target P. falciparum, the species associated with high mortality rates and severe clinical symptoms, non-falciparum species exhibit different transmission dynamics, remain hugely neglected, and pose a significant challenge to malaria elimination efforts. Recent studies have reported the presence of antigens associated with cross-protective immunity, which can potentially disrupt the transmission of various Plasmodium species. With the sequencing of the Plasmodium genome and the development of immunoinformatic tools, in this study, we sought to exploit the evolutionary history of Plasmodium species to identify conserved cross-species B-cell linear epitopes in merozoite proteins. We retrieved Plasmodium proteomes associated with human malaria and applied a subtractive proteomics approach focusing on merozoite stage proteins. Bepipred 2.0 and Epidope were used to predict B-cell linear epitopes using P. falciparum as the reference species. The predictions were further compared against human and non-falciparum databases and their antigenicity, toxicity, and allergenicity assessed. Subsequently, epitope conservation was carried out using locally sequenced P. falciparum isolates from a malaria-endemic region in western Kenya (n=27) and Kenyan isolates from MalariaGEN version 6 (n=131). Finally, physiochemical characteristics and tertiary structure of the B-cell linear epitopes were determined. The analysis revealed eight epitopes that showed high similarity (70-100%) between falciparum and non-falciparum species. These epitopes were highly conserved when assessed across local isolates and those from the MalariaGEN database and showed desirable physiochemical properties. Our results show the presence of conserved cross-species B-cell linear epitopes that could aid in targeting multiple Plasmodium species. Nevertheless, validating their efficacy in-vitro and in-vivo experimentally is essential.
DNA methylation regulates B cell activation via repressing Pax5 expression in teleost
Authors: Shi Yuan , Zhu Zhuo , Chen Qiuxuan , Chen Xinhua
Published: February 2024

In mammals, the transcription factor Pax5 is a key regulator of B cell development and maturation and specifically expressed in naive/mature B cells but repressed upon B cell activation. Despite the long-standing proposal that Pax5 repression is essential for proper B cell activation, the underlying mechanisms remain largely elusive. In this study, we used a teleost model to elucidate the mechanisms governing Pax5 repression during B cell activation. Treatment with lipopolysaccharide (LPS) and chitosan oligosaccharide (COS) significantly enhanced the antibody secreting ability and phagocytic capacity of IgM+ B cells in large yellow croaker (Larimichthys crocea), coinciding with upregulated expression of activation-related genes, such as Bcl6, Blimp1, and sIgM, and downregulated expression of Pax5. Intriguingly, two CpG islands were identified within the promoter region of Pax5. Both CpG islands exhibited hypomethylation in naive/mature B cells, while CpG island1 was specifically transited into hypermethylation upon B cell activation. Furthermore, treatment with DNA methylation inhibitor 5-aza-2’-deoxycytidine (AZA) prevented the hypermethylation of CpG island1, and concomitantly impaired the downregulation of Pax5 and activation of B cells. Finally, through in vitro methylation experiments, we demonstrated that DNA methylation exerts an inhibitory effect on promoter activities of Pax5. Taken together, our findings unveil a novel mechanism underlying Pax5 repression during B cell activation, thus promoting the understanding of B cell activation process.
Rapid variations of phytoplankton blooms and their dynamics off the Changjiang River Estuary
Authors: Xu Miaomiao , Wang Yihe , Feng Zhixuan , Wu Hui
Published: February 2024

Phytoplankton frequently blooms in estuaries and coastal seas. Numerous dynamic processes affect these regions, generating complex hydrodynamics that induce intense phytoplankton variability over multiple time scales. Especially, the variability over time scales of 100-101 days (event-scale) is a strong signal that is fundamental to coastal aquatic environments and ecosystems. Based on the historical monitoring of harmful algal bloom events and a fully coupled hydrodynamics-sediment-ecosystem numerical model, this study explored horizontal distribution patterns of the phytoplankton maximum off the Changjiang River Estuary over multiple time scales. Our results showed that the bloom events typically lasted less than a week and horizontal distribution of the horizontal chlorophyll maximum varied over the time scale of days. Tidal forcing was shown to dominate the periodic phytoplankton variability. The variations of river runoff and wind forcing also modulated this variability and added more disturbances. Increased runoff and enhanced summer monsoon wind caused the horizontal chlorophyll maximum to physically extend further offshore, while they also biologically stimulated phytoplankton blooms. The analysis of the time scale showed that the regulation of horizontal chlorophyll maximum responds faster to physical effects than in biological ones. At the same time, during neap tides, the adjustment of phytoplankton to the disturbances associated with the hydrodynamic processes was stably salient. Such adjustment was based on the adaptation to light availability and nutrient supply. This study contributes to the understanding of phytoplankton variability in estuaries affected by multiple physical-biological processes over the time scale of days and benefits to the management of environmental conservation.
Transcriptome analysis reveals ABA involved in the detoxification mechanism of macroalga Gracilariopsis lemaneiformis to cadmium toxicity
Authors: Chen Xiaojiao , Tang Yueyao , Sun Xue , Zhang Hao , Xu Nianjun
Published: February 2024

Introduction

Cadmium (Cd) is a significant threat environmental pollutant in the marine ecological environment offshore. The macroalga, Gracilariopsis lemaneiformis, of significant economic value, is widely cultivated along China’s coastline. Yet, little is known about the molecular mechanisms underlying Cd tolerance in macroalga.

Methods

Here, we examined the transcriptome of G. lemaneiformis exposed to Cd to identify the responses to Cd stress.

Results and discussion

Our findings revealed that Cd led to the retardation of growth rate in G. lemaneiformis, accompanied by a notable reduction in the content of photosynthetic pigments and a decrease in the expression of genes associated with the photosynthetic system and nitrogen metabolism. When exposed to Cd, there was a rapid increase in Cd levels through the upregulation of genes encoding GlZIP6 and GlIRT1. Additionally, the expression of Cd efflux transporters, GlZIP1 and GlABCG22, and the ABCC7 transporter for compartmentation to the vacuole, was induced to mitigate Cd toxicity. Cd also activated crucial genes involved in the ABA biosynthesis and enhanced ABA content, thereby inducing ABA signaling pathway. Furthermore, exogenous ABA reduced the growth inhibition of G. lemaneiformis under Cd stress. Redox homeostasis was adjusted to adapt to Cd toxicity, with thioredoxin, glutaredoxin cycle and ascorbate-glutathione cycle identified as playing significant in maintaining reactive oxygen species homeostasis. Moreover, transcription factors such as several MYBs, signal transmission factors G protein and heat shock proteins (sHSPs, HSP 40, HSP 90, HSP101) were involved in the detoxification of Cd. Collectively, this study provided a comprehensive understanding of the molecular mechanisms underpinning the of responses of macroalga G. lemaneiformis to Cd exposure.
Wave, light, and dissolved oxygen exposures drive novel coastal eelgrass (Zostera pacifica) transplant performance
Authors: Sanders Rilee D. , Obaza Adam K. , Grime Benjamin C. , Lindhart Mathilde , Miller Luke P. , Elsmore Kristen E. , Carmack Olivia C. , Ford Tom K. , Leichter James J.
Published: February 2024

The high ecological and economic value of seagrass has been long recognized, with these foundational habitats providing myriad ecosystem services. Yet through cumulative anthropogenic impacts, seagrasses are exhibiting extensive declines globally. A litany of studies and active restoration trials have demonstrated practical methodologies to restore seagrass habitats and effectively return critical habitat functions to degraded coastal zone systems worldwide. Seagrass loss along the U.S. West Coast has precipitated decades of seagrass protection, conservation, and restoration efforts. Yet, mitigation transplanting efforts have prioritized Zostera marina (narrow-leaved eelgrass) in shallow, protected environments, while a dearth of information is available on species inhabiting offshore islands and exposed mainland coasts. In this study, we conducted a novel transplant of Zostera pacifica, a wide-leaved species found in depths of 7 – 20 m along the offshore islands and mainland coast of California. Transplants were conducted at three geographically distinct sites in Santa Monica Bay, coupled with continuous monitoring of biophysical parameters providing insight into physical drivers at transplant and donor sites. Utilizing in situ data, and environmental thresholds adapted from the literature for Z. marina, we performed exposure analyses to evaluate factors influencing Z. pacifica transplant performance. Exceedances of threshold values for environmental parameters, specifically, wave exposure and near-bed flow speeds (Hrms > 0.59 m and Urms > 0.1 m s-1), photosynthetically active radiation (< 3 and > 5 mol m-2 day-1) and dissolved oxygen (< 3 mg O2 L-1) exposure impacted transplant survivorship. These results suggest Z. pacifica persist in biophysically dynamic conditions and are sensitive to exceedances of thresholds, underlining the importance of pre-transplant site-selection processes to this species. These data represent the first holistic study of Z. pacifica transplanting on an exposed mainland coast, which provides a view into the baseline environmental envelopes within existing Z. pacifica habitat, and further, may serve as a model for investigating scalable open coast seagrass restoration for temperate regions.
Antagonistic properties of Lactiplantibacillus plantarum MYSVB1 against Alternaria alternata: a putative probiotic strain isolated from the banyan tree fruit
Authors: Vasundaradevi R. , Sarvajith M. , Somashekaraiah Rakesh , Gunduraj Adithi , Sreenivasa M. Y.
Published: February 2024

Alternaria alternata, a notorious phytopathogenic fungus, has been documented to infect several plant species, leading to the loss of agricultural commodities and resulting in significant economic losses. Lactic acid bacteria (LAB) hold immense promise as biocontrol candidates. However, the potential of LABs derived from fruits remains largely unexplored. In this study, several LABs were isolated from tropical fruit and assessed for their probiotic and antifungal properties. A total of fifty-five LABs were successfully isolated from seven distinct fruits. Among these, seven isolates showed inhibition to growth of A. alternata. Two strains, isolated from fruits: Ficus benghalensis, and Tinospora cordifolia exhibited promising antifungal properties against A. alternata. Molecular identification confirmed their identities as Lactiplantibacillus plantarum MYSVB1 and MYSVA7, respectively. Both strains showed adaptability to a wide temperature range (10–45°C), and salt concentrations (up to 7%), with optimal growth around 37 °C and high survival rates under simulated gastrointestinal conditions. Among these two strains, Lpb. plantarum MYSVB1 demonstrated significant inhibition (p < 0.01) of the growth of A. alternata. The inhibitory effects of cell-free supernatant (CFS) were strong, with 5% crude CFS sufficient to reduce fungal growth by >70% and complete inhibition by 10% CFS. Moreover, the CFS was inhibitory for both mycelial growth and conidial germination. CFS retained its activity even after long cold storage. The chromatographic analysis identified organic acids in CFS, with succinic acid as the predominant constituent, with lactic acid, and malic acid in descending order. LAB strains isolated from tropical fruits showed promising probiotic and antifungal properties, making them potential candidates for various applications in food and agriculture.
Halotolerant and plant growth-promoting endophytic fungus Aspergillus terreus CR7 alleviates salt stress and exhibits genoprotective effect in Vigna radiata
Authors: Chauhan Pooja , Singh Mandeep , Sharma Avinash , Singh Mangaljeet , Chadha Pooja , Kaur Amarjeet
Published: February 2024

Soil salinity is one of the major environmental stresses that results in reduction of cultivable land and decreased productivity. In the present study, halotolerant and plant growth-promoting endophytic fungi were isolated from Catharanthus roseus, and their effect in mitigating salt stress in Vigna radiata was evaluated. An isolate CR7, identified to be Aspergillus terreus, showing plant growth promotion activities, viz. IAA production (23.43 ± 0.79 μg/ml), phosphate solubilization (133.63 ± 6.40 μg/ml), ACC deaminase activity (86.36 ± 2.70 μmol α-ketobutyrate/h/mg protein) etc. and ability to grow at 15% NaCl was selected for further in vivo studies. Colonization of CR7 was carried out in V. radiata which was subjected to different concentrations of salt (150, 200, and 250 mM NaCl). Under salt stress, A. terreus CR7 inoculated plants showed substantially improved root and shoot length, biomass, chlorophyll content, relative water content, phenolics, protein content, and DPPH scavenging activity. Endogenous IAA level was enhanced by 5.28-fold in treated plants at maximum salt stress. Inoculation of A. terreus CR7 affected oxidative stress parameters, exhibiting an increase in catalase and superoxide dismutase and reduction in proline, electrolyte leakage, and malondialdehyde content. Fluorescent microscopic analysis of roots revealed improved cell viability and decreased levels of glutathione and hydrogen peroxide under salt stress in treated plants. The isolate A. terreus CR7 also protected against DNA damage induced by salt stress which was evaluated using comet assay. A decrease in DNA tail length, tail moment, and olive tail moment to the extent of 19.87%, 19.76%, and 24.81%, respectively, was observed in A. terreus CR7-colonized plants under salt stress. It can be concluded that A. terreus CR7 can be exploited for alleviating the impact of salt stress in crop plants.
Effects of type of substrate and dilution rate on fermentation in serial rumen mixed cultures
Authors: Ungerfeld Emilio M. , Cancino-Padilla Nathaly , Vera-Aguilera Nelson , Scorcione M. Carolina , Saldivia Marcelo , Lagos-Pailla Lorena , Vera Milena , Cerda Cristián , Muñoz Camila , Urrutia Natalie , Martínez Emilio D.
Published: February 2024

Forages and concentrates have consistently distinct patterns of fermentation in the rumen, with forages producing more methane (CH4) per unit of digested organic matter (OM) and higher acetate to propionate ratio than concentrates. A mechanism based on the Monod function of microbial growth has been proposed to explain the distinct fermentation pattern of forages and concentrates, where greater dilution rates and lower pH associated with concentrate feeding increase dihydrogen (H2) concentration through increasing methanogens growth rate and decreasing methanogens theoretically maximal growth rate, respectively. Increased H2 concentration would in turn inhibit H2 production, decreasing methanogenesis, inhibit H2-producing pathways such as acetate production via pyruvate oxidative decarboxylation, and stimulate H2-incorporating pathways such as propionate production. We examined the hypothesis that equalizing dilution rates in serial rumen cultures would result in a similar fermentation profile of a high forage and a high concentrate substrate. Under a 2 × 3 factorial arrangement, a high forage and a high concentrate substrate were incubated at dilution rates of 0.14, 0.28, or 0.56 h−1 in eight transfers of serial rumen cultures. Each treatment was replicated thrice, and the experiment repeated in two different months. The high concentrate substrate accumulated considerably more H2 and formate and produced less CH4 than the high forage substrate. Methanogens were nearly washed-out with high concentrate and increased their initial numbers with high forage. The effect of dilution rate was minor in comparison to the effect of the type of substrate. Accumulation of H2 and formate with high concentrate inhibited acetate and probably H2 and formate production, and stimulated butyrate, rather than propionate, as an electron sink alternative to CH4. All three dilution rates are considered high and selected for rapidly growing bacteria. The archaeal community composition varied widely and inconsistently. Lactate accumulated with both substrates, likely favored by microbial growth kinetics rather than by H2 accumulation thermodynamically stimulating electron disposal from NADH into pyruvate reduction. In this study, the type of substrate had a major effect on rumen fermentation largely independent of dilution rate and pH.
The Locare workflow: representing neuroscience data locations as geometric objects in 3D brain atlases
Authors: Blixhavn Camilla H. , Reiten Ingrid , Kleven Heidi , Øvsthus Martin , Yates Sharon C. , Schlegel Ulrike , Puchades Maja A. , Schmid Oliver , Bjaalie Jan G. , Bjerke Ingvild E. , Leergaard Trygve B.
Published: February 2024

Neuroscientists employ a range of methods and generate increasing amounts of data describing brain structure and function. The anatomical locations from which observations or measurements originate represent a common context for data interpretation, and a starting point for identifying data of interest. However, the multimodality and abundance of brain data pose a challenge for efforts to organize, integrate, and analyze data based on anatomical locations. While structured metadata allow faceted data queries, different types of data are not easily represented in a standardized and machine-readable way that allow comparison, analysis, and queries related to anatomical relevance. To this end, three-dimensional (3D) digital brain atlases provide frameworks in which disparate multimodal and multilevel neuroscience data can be spatially represented. We propose to represent the locations of different neuroscience data as geometric objects in 3D brain atlases. Such geometric objects can be specified in a standardized file format and stored as location metadata for use with different computational tools. We here present the Locare workflow developed for defining the anatomical location of data elements from rodent brains as geometric objects. We demonstrate how the workflow can be used to define geometric objects representing multimodal and multilevel experimental neuroscience in rat or mouse brain atlases. We further propose a collection of JSON schemas (LocareJSON) for specifying geometric objects by atlas coordinates, suitable as a starting point for co-visualization of different data in an anatomical context and for enabling spatial data queries.
Quantitative evaluation of embedding resins for volume electron microscopy
Authors: Tegethoff Lennart , Briggman Kevin L.
Published: February 2024

Optimal epoxy resin embedding is crucial for obtaining consistent serial sections from large tissue samples, especially for block faces spanning >1 mm2. We report a method to quantify non-uniformity in resin curing using block hardness measurements from block faces. We identify conditions that lead to non-uniform curing as well as a procedure to monitor the hardness of blocks for a wide range of common epoxy resins used for volume electron microscopy. We also assess cutting repeatability and uniformity by quantifying the transverse and sectional cutting forces during ultrathin sectioning using a sample-mounted force sensor. Our findings indicate that screening and optimizing resin formulations is required to achieve the best repeatability in terms of section thickness. Finally, we explore the encapsulation of irregularly shaped tissue samples in a gelatin matrix prior to epoxy resin embedding to yield more uniform sections.
Successful avatrombopag combined with cyclosporine treatment for carboplatin/pegylated liposomal doxorubicin/bevacizumab-induced acquired amegakaryocytic thrombocytopenia in a patient with recurrent ovarian cancer: case report
Authors: Meng Weikang , Hua Jinsheng , Wang Jiabing
Published: February 2024

Carboplatin/pegylated liposomal doxorubicin/bevacizumab is an accepted standard anti-cancer treatment option for recurrent ovarian cancer. However, the occurrence of adverse events associated with this therapeutic regimen limits its continued clinical use. Among these adverse events, acquired amegakaryocytic thrombocytopenia is a rare but often potentially life-threatening adverse effect, and is intolerant to multiple treatment approaches. We report, for the first time, the successful treatment using avatrombopag combined with cyclosporine in one case of carboplatin/pegylated liposomal doxorubicin/bevacizumab-induced acquired amegakaryocytic thrombocytopenia, which was refractory or intolerant to glucocorticoids, intravenous immunoglobulin, recombinant human thrombopoietin, androgen, and even thrombopoietin receptor receptor agonist eltrombopag and herombopag. To date, this case manifests as normal platelet counts that are independent of transfusion. Our findings suggest that this combination is a potential and valuable alternative in acquired amegakaryocytic thrombocytopenia.
An immune-related gene prognostic prediction risk model for neoadjuvant chemoradiotherapy in rectal cancer using artificial intelligence
Authors: Shu Pei , Liu Ning , Luo Xu , Tang Yuanling , Chen Zhebin , Li Dandan , Miao Dong , Duan Jiayu , Yan Ouying , Sheng Leiming , Ouyang Ganlu , Wang Sen , Jiang Dan , Deng Xiangbing , Wang Ziqiang , Li Qingyun , Wang Xin
Published: February 2024

Background

This study aimed to establish and validate a prognostic model based on immune-related genes (IRGPM) for predicting disease-free survival (DFS) in patients with locally advanced rectal cancer (LARC) undergoing neoadjuvant chemoradiotherapy, and to elucidate the immune profiles associated with different prognostic outcomes.

Methods

Transcriptomic and clinical data were sourced from the Gene Expression Omnibus (GEO) database and the West China Hospital database. We focused on genes from the RNA immune-oncology panel. The elastic net approach was employed to pinpoint immune-related genes significantly impacting DFS. We developed the IRGPM for rectal cancer using the random forest technique. Based on the IRGPM, we calculated prognostic risk scores to categorize patients into high-risk and low-risk groups. Comparative analysis of immune characteristics between these groups was conducted.

Results

In this study, 407 LARC samples were analyzed. The elastic net identified a signature of 20 immune-related genes, forming the basis of the IRGPM. Kaplan−Meier survival analysis revealed a lower 5-year DFS in the high-risk group compared to the low-risk group. The receiver operating characteristic (ROC) curve affirmed the model’s robust predictive capability. Validation of the model was performed in the GSE190826 cohort and our institution’s cohort. Gene expression differences between high-risk and low-risk groups predominantly related to cytokine−cytokine receptor interactions. Notably, the low-risk group exhibited higher immune scores. Further analysis indicated a greater presence of activated B cells, activated CD8 T cells, central memory CD8 T cells, macrophages, T follicular helper cells, and type 2 helper cells in the low-risk group. Additionally, immune checkpoint analysis revealed elevated PDCD1 expression in the low-risk group.

Conclusions

The IRGPM, developed through random forest and elastic net methodologies, demonstrates potential in distinguishing DFS among LARC patients receiving standard treatment. Notably, the low-risk group, as defined by the IRGPM, showed enhanced activation of adaptive immune responses within the tumor microenvironment.