bluuebunny/crossref_metadata_2025 huggingface dataset:
Machine learning models for predicting steroid-resistant of nephrotic syndrome
Authors: Ye Qing , Li Yuzhou , Liu Huihui , Mao Jianhua , Jiang Hangjin
Published: January 2023

Background

In the absence of effective measures to predict steroid responsiveness, patients with nonhereditary steroid-resistant nephrotic syndrome (SRNS) have a significantly increased risk of progression to end-stage renal disease. In view of the poor outcomes of SRNS, it is urgent to identify the steroid responsiveness of idiopathic nephrotic syndrome (INS) early.

Methods

To build a prediction model for SRNS, we collected 91 subjects; 57 of them had steroid-sensitive nephrotic syndrome, and the others had SRNS. For each subject, 87 clinical variables were measured. In general, only a small part of these variables is informative to SRNS. Thus, we proposed a new variable selection framework including a penalized regression approach (named MLR+TLP) to select variables having a linear effect on the SRNS and a nonparametric screening method (MAC) to select variables having a nonlinear marginal (joint) effect on the SRNS. Thereafter, considering the correlation between selected clinical variables, we used a stepwise method to build our final model for predicting SRNS. In addition, a statistical testing procedure is proposed to test the overfitting of the proposed model.

Results

Twenty-six clinical variables were selected to be informative to SRNS, and an SVM model was built to predict SRNS with a leave-one-out cross-validation (LOO-CV) accuracy of 95.2% (overfitting p value<0.005). To make the model more useful, we incorporate prior medical information into the model and consider the correlation between selected variables. Then, a reduced SVM model including only eight clinical variables (erythrocyte sedimentation rate, urine occult blood, percentage of neutrophils, immunoglobulin A, cholesterol, vinculin autoantibody, aspartate aminotransferase, and prolonged prothrombin time) was built to have a LOO-CV accuracy of 92.8% (overfitting p value<0.005). The validation cohort showed that the reduced model obtained an accuracy of 94.0% (overfitting p value<0.005), with a sensitivity of 90.0% and a specificity of 96.7%. Notably, vinculin autoantibody is the only podocyte autoantibody included in this model. It is linearly related to steroid responsiveness. Finally, our model is freely available as a user-friendly web tool at https://datalinkx.shinyapps.io/srns/.

Conclusion

The SRNS prediction model constructed in this study comprehensively and objectively evaluates the internal conditions and disease status of INS patients and will provide scientific guidance for selecting treatment methods for children with nonhereditary SRNS.
Smoking and coronary artery disease risk in patients with diabetes: A Mendelian randomization study
Authors: Chen Songzan , Yang Fangkun , Xu Tian , Wang Yao , Zhang Kaijie , Fu Guosheng , Zhang Wenbin
Published: January 2023

Background

Previous observational studies have shown an association between smoking and coronary artery disease (CAD) in patients with diabetes. Whether this association reflects causality remains unestablished. This study aimed to explore the causal effect of smoking on CAD in patients with diabetes.

Methods

Genetic signatures for smoking were extracted from a large genome-wide association study (GWAS), consisted of up to 1.2 million participants. Four smoking phenotypes were included: smoking initiation, cigarettes per day, age at initiation of regular smoking, and smoking cessation. Genetic associations with CAD in patients with diabetes were extracted from another GWAS, which included 15,666 participants (3,968 CAD cases and 11,696 controls). The analyses were performed using the univariable and multivariable Mendelian randomization (MR) method.

Results

MR analysis revealed that smoking initiation was positively related to CAD risk in patients with diabetes (OR = 1.322, 95% CI = 1.114 – 1.568, P = 0.001), but this association was attenuated when adjusted for cardiovascular risk factors (OR = 1.212, 95% CI = 1.008 – 1.457, P = 0.041). Age at initiation of regular smoking was negatively related to CAD in patients with diabetes (OR = 0.214, 95% CI = 0.070 – 0.656, P = 0.007), but this association became insignificant when adjusted for cardiovascular risk factors.

Conclusions

This study supported the effect of smoking initiation on the risk of CAD in patients with diabetes.
Environmental variability and governance: The fishery of Octopus maya in Yucatan, Mexico
Authors: Santamaría Antonio , Euán Ávila Jorge I. , Munguia-Rosas Miguel A. , Saldívar-Lucio Romeo , Fraga Julia
Published: January 2023

In the socio-ecological system of the Mayan octopus, climate change, natural variability and human decisions impact the dynamics and population structure of the octopus. Since fishing decisions have been made out of synchrony concerning the octopus’s natural response, the system’s sustainability is put at risk. Sustainability is a socially desirable, environmentally necessary, and economically viable goal; since it contributes positively to food security, ways, and lifestyles. The objective of this work is to deepen the study of the perception of the fishermen of Progreso, Yucatán regarding the interactions between the Mayan octopus, the variability in the environment, the governance system, and fishing decisions. It was developed from a qualitative and quantitative approach, and bonds of trust were created for a year adopting an ethnographic approach to deepen the use of language, feelings, and emotions. To obtain information, open and semi-structured interviews, participant observation, and documentary research were carried out. For the analysis and evaluation of perceptions and fishing decisions, a non-parametric test was used through the modeling of structural equations with Partial Least Squares (PLS). It was found that, although the quantity to be captured is strongly influenced by the market, the strong incidence of changes in the environment on capture decisions stands out among the results. The experiences and knowledge of the fishermen about the marine environment represent an opportunity to contribute to the process of evolution of the socio-ecological system of the Mayan octopus, towards the establishment of norms and agreements between the different actors and contribute to the construction of resilience and sustainability against the overexploitation and environmental variability.
Long-term over-the-horizon microwave channel measurements and statistical analysis in evaporation ducts over the Yellow Sea
Authors: Wang Shuwen , Yang Kunde , Shi Yang , Zhang Hao , Yang Fan , Hu Dawei , Dong Guoyu , Shu Yihang
Published: January 2023

Maritime high-speed over-the-horizon wireless communication is realizable through evaporation ducts. Detailed measurement, analysis, and modeling of duct channels are essential for application of this communication technique. In this paper, X-band electromagnetic (EM) wave propagation systems were developed and deployed for a 133-km over-the-horizon microwave link in coastal areas of the Yellow Sea. The propagation length was 7.7 times the line-of-sight length. Measurement results including the path loss (PL) and meteorological data were obtained during a 54-day period in autumn 2021. The long-term channel results were analyzed on the basis of statistical analysis and model simulations. Results showed that our measurement system, with a maximum measurable power loss of 200 dB, had connected with a probability of 56.2% during the measurement period. Model simulation showed that evaporation duct environments are not ideal in autumn, with an average evaporation duct height (EDH) of 10.6 m. The land breeze in autumn introduced dry and cold air to the link, which could promote evaporation of seawater and reduce PL by approximately 40 dB. Annual spatiotemporal characteristics of EDH showed that evaporation ducts are most suitable for over-the-horizon communication in spring, especially May.
Observational studies of the effects of wind mixing and biological process on the vertical distribution of dissolved oxygen off the Changjiang Estuary
Authors: Miao Yanyi , Wang Bin , Li Dewang , Sun Xiangyu , Xu Zhongsheng , Sun Qianwen , Jiang Zhibing , Ma Xiao , Jin Haiyan , Chen Jianfang
Published: January 2023

Wind mixing is important in regulating dissolved oxygen (DO) variability; however, the transect response of DO dynamics to wind disturbance has seldom been documented with field data. In the summer of 2017, repeat transect observations off the Changjiang Estuary were conducted throughout a fresh wind (the maximum wind speed was 9.8 m s–1) event to reveal the role of physical mixing and biological activity in DO variations. After the wind event, hypoxia was alleviated presenting as the hypoxia thickness decreased from 30 m to 20 m. However, poorly ventilated near-bottom hypoxia was aggravated with a further decrease in DO. Generally, the saturation of dissolved oxygen (DOs) in depth-integrated water column increased by 9%–49% through physical diffusion with a weakened stratification and enhanced phytoplankton bloom. However, in this case, the wind-induced physical water mass mixing by transporting DO downward had a limited contribution to the water-column DO budget, while upwards nutrients induced by mixing fueled the larger vertical area of algae bloom and subsequent substantial oxygen consumption. As the wind speed increased, the air-sea exchange would be important in supplying DO, especially in nearshore areas, which could effectively offset the DO deficiency. In summary, frequently occurring fresh wind-mixing events off the Changjiang Estuary would alleviate hypoxia in the water column but probably exacerbate hypoxia at the bottom, as determined by competing ventilation and respiration roles. Such complex interactions likely occur and perform differently as wind stress varies. Thus, high-spatial and long-term process observations are required to better understand the net effects of bottom hypoxia evolution.
Surfacing rates, swim speeds, and patterns of movement of Antarctic blue whales
Authors: Calderan Susannah V. , Leaper Russell , Andrews-Goff Virginia , Miller Brian S. , Olson Paula A. , Reyes M. V. Reyes , Bell Elanor , Double Michael C.
Published: January 2023

During three surveys in the austral summers of 2013, 2015, 2019, data on Antarctic blue whale blow rates, dive times, swim speeds, and broadscale movements were collected using video photogrammetric tracking and intra-voyage photo-identification. A total of 24.4 hours of video observations were suitable for blow interval or movement analysis. Similar to other blue whale populations, Antarctic blue whale dive behaviour comprised a sequence of short dives followed by a long dive with a mean dive time for short dives of 17.6 s, and a mean long dive time of 189.3 s. Two separate methods were used to estimate the average blow rate for Antarctic blue whales, giving estimates of 59.7 and 63.2 blows per hour. The overall mean swim speed over the course of all suitable video track segments was 1.59 ms-1, but there were significant differences between years in the mean of the overall movement rate for each track; average movement rates were lower in 2015 compared to 2013 and 2019 (0.90 ms-1, 1.84 and 1.55 ms-1respectively), with higher rates of turning in 2015. In 2019, there was faster overall movement through the study area in a consistent direction. The total number of photo-identified blue whales re-sighted intra-season in 2013 was nine (out of 50 identified individuals); in 2015 it was seven (out of 46); in 2019 two (out of 25). Whales remained for several days with little overall movement within the 2015 study area, whereas they were moving through the study area in 2019, which would explain the low number of intra-season resights. The predominant heading in 2019 was towards the area of Antarctic blue whale concentrations at the entrance to the Ross Sea observed in previous years. The photo-identification data also show a high proportion of resighted whales with coherent movements. This suggests that Antarctic blue whales might travel together, at least over periods of several days or sometimes up to a month. The differences between behaviours in 2015 and 2019 in particular may be related to differences in the characteristics of krill swarms between the study areas.
Biomass prediction method of nuclear power cold source disaster based on deep learning
Authors: Huo Jianling , Li Chao , Liu SongTang , Sun Lei , Yang Lei , Song Yuze , Li Jun
Published: January 2023

Given the insufficient early warning capacity of nuclear cold source biological disasters, this paper explores prediction methods for biomass caused by nuclear cold source disasters based on deep learning. This paper also uses the correlation analysis method to determine the main environmental factors. The adaptive particle swarm optimization method was used to optimize the depth confidence network model of the Gaussian continuous constrained Boltzmann machine (APSO-CRBM-DBN). To train the model, the marine environmental factors were used as the main input factors and the biomass after a period of time was used as the output for training. Optimal prediction results were obtained, and thus, the prediction model of biomass caused by the nuclear cold source disaster was established. The model provides an accurate scientific basis for the early warning of cold source disasters in nuclear power plants and has important practical significance for solving the problem of biological blockage at the inlet of cold source water in nuclear power plants.
Drought alleviation efficacy of a galactose rich polysaccharide isolated from endophytic Mucor sp. HELF2: A case study on rice plant
Authors: Santra Hiran Kanti , Banerjee Debdulal
Published: January 2023

Endophytes play a vital role in plant growth under biotic and abiotic stress conditions. In the present investigation, a Galactose-Rich Heteropolysaccharide (GRH) with a molecular weight of 2.98 × 105 Da was isolated from endophytic Mucor sp. HELF2, a symbiont of the East Indian screw tree Helicteres isora. OVAT (One Variable at A Time) experiment coupled with RSM (Response Surface Methodology) study exhibited 1.5-fold enhanced GRH production (20.10 g L−1) in supplemented potato dextrose broth at a pH of 7.05 after 7.5 days of fermentation in 26°C. GRH has alleviated drought stress (polyethylene glycol induced) in rice seedlings (Oryza sativa ssp. indica MTU 7093 swarna) by improving its physicochemical parameters. It has been revealed that spray with a 50-ppm dosage of GRH exhibited an improvement of 1.58, 2.38, 3, and 4 times in relative water contents and fresh weight of the tissues, root length, and shoot length of the rice seedlings, respectively “in comparison to the control”. Moreover, the soluble sugars, prolines, and chlorophyll contents of the treated rice seedlings were increased upto 3.5 (0.7 ± 0.05 mg/g fresh weight), 3.89 (0.57 ± 0.03 mg/g fresh weight), and 2.32 (1,119 ± 70.8 μg/gm of fresh weight) fold respectively, whereas malondialdehyde contents decreased up to 6 times. The enzymatic antioxidant parameters like peroxidase and superoxide dismutase and catalase activity of the 50 ppm GRH treated seedlings were found to be elevated 1.8 (720 ± 53 unit/gm/min fresh weight), 1.34 (75.34 ± 4.8 unit/gm/min fresh weight), and up to 3 (100 ppm treatment for catalase – 54.78 ± 2.91 unit/gm/min fresh weight) fold, respectively. In this context, the present outcomes contribute to the development of novel strategies to ameliorate drought stress and could fortify the agro-economy of India.
Efficacy of a recombinant turkey herpesvirus (H9) vaccine against H9N2 avian influenza virus in chickens with maternal-derived antibodies
Authors: Pan Xue , Liu Qinfang , Niu Shiqi , Huang Dongming , Yan Dawei , Teng Qiaoyang , Li Xuesong , Beerens Nancy , Forlenza Maria , de Jong Mart C. M. , Li Zejun
Published: January 2023

Although vaccines have been widely used for many years, they have failed to control H9N2 avian influenza virus (AIV) in the field in China. The high level of maternal-derived antibodies (MDAs) against H9N2 virus contributes to the H9N2 influenza vaccine failure in poultry. The study aimed to generate a new vaccine to overcome MDAs interference in H9N2 vaccination in chickens. We used turkey herpesvirus (HVT) as a vaccine vector to express H9 hemagglutinin (HA) proteins. The recombinant HVT expressing H9 HA proteins (rHVT-H9) was successfully generated and characterized in primary chicken embryonic fibroblasts (CEFs). Western blot and indirect immunofluorescence assay (IFA) showed that the rHVT-H9 consistently expressed HA proteins. In addition, the rHVT-H9 had similar growth kinetics to the parent HVT. Preliminary animal experiments showed that compared to the conventional inactivated whole virus (IWV) vaccine, the rHVT-H9 stimulated robust humoral immunity in chickens with passively transferred antibodies (PTAs) that were used to mimic MDAs. Transmission experiments showed that the rHVT-H9 induced both humoral and cellular immunity in chickens with PTAs. Furthermore, we used mathematical models to quantify the vaccine’s efficacy in preventing the transmission of H9N2 AIV. The results showed that the rHVT-H9 reduced the virus shedding period and decreased the reproduction ratio (R) value in chickens with PTAs after homologous challenge. However, the vaccination in this trial did not yet bring R < 1. In summary, we generated a new rHVT-H9 vaccine, which stimulated strong humoral and cellular immunity, reducing virus shedding and transmission of H9N2 AIV even in the presence of PTAs in chickens.
Bark-inhabiting fungal communities of European chestnut undergo substantial alteration by canker formation following chestnut blight infection
Authors: Douanla-Meli Clovis , Moll Julia
Published: January 2023

Background

Chestnut forests are severely threatened by chestnut blight caused by the fungal pathogen Cryphonectria parasitica and the infected trees exhibit bark canker in the later stage of the disease. European chestnut (Castanea sativa) is further infected by Gnomoniopsis smithogilvyi, another canker-causing fungal pathogen. We explored whether and how chestnut blight is reflected in bark-inhabiting fungal communities of European chestnut and also assessed the co-occurrence of C. parasitica and G. smithogilvyi.

Materials and methods

We initially investigated the fungal communities of European chestnut bark tissues and further monitored changes in these fungal communities with regard to disease progression from infection to canker formation by analyzing bark samples from asymptomatic trees, asymptomatic trees with latent C. parasitica infection, and infected trees with canker tissues, using amplicon sequencing of the ITS2 region of rDNA.

Results

The results showed that fungal community composition and diversity differed between the sample types. The fungal community composition was substantially reshaped by canker formation, whereas latent C. parasitica infection and more specifically pre-canker infection period per se had a weak effect. Fungal communities of canker samples was less diverse and more dissimilar to those of other sample types. C. parasitica dominated the mycobiome of canker samples, whereas G. smithogilvyi was found in only 9% of canker samples at very low abundances. However, G. smithogilvyi was a dominant fungus in the bark of healthy plants.

Conclusion

This study highlights that canker formation is the principal driver of decreasing diversity and altered composition of the mycobiome in bark tissues of European chestnut infected by C. parasitica infection. It additionally emphasizes the scarce co-occurrence of C. parasitica and G. smithogilvyi on European chestnut.
The incorporation of Mg2+ ions into aragonite during biomineralization: Implications for the dolomitization of aragonite
Authors: Han Zuozhen , Meng Ruirui , Zhao Hui , Gao Xiao , Zhao Yanyang , Han Yu , Liu Fang , Tucker Maurice E. , Deng Jiarong , Yan Huaxiao
Published: January 2023

Bacteria can facilitate the increase of Mg2+ content in biotic aragonite, but the molecular mechanisms of the incorporation of Mg2+ ion into aragonite facilitated by bacteria are still unclear and the dolomitization of aragonite grains is rarely reported. In our laboratory experiments, the content of Mg2+ ions in biotic aragonite is higher than that in inorganically-precipitated aragonite and we hypothesize that the higher Mg content may enhance the subsequent dolomitization of aragonite. In this study, biotic aragonite was induced by Bacillus licheniformis Y1 at different Mg/Ca molar ratios. XRD data show that only aragonite was precipitated in the media with Mg/Ca molar ratios at 6, 9, and 12 after culturing for 25 days. The EDS and atomic absorption results show that the content of Mg2+ ions in biotic aragonite increased with rising Mg/Ca molar ratios. In addition, our analyses show that the EPS from the bacteria and the organics extracted from the interior of the biotic aragonite contain the same biomolecules, including Ala, Gly, Glu and hexadecanoic acid. The content of Mg2+ ions in the aragonite precipitates mediated by biomolecules is significantly higher than that in inorganically-precipitated aragonite. Additionally, compared with Ala and Gly, the increase of the Mg2+ ions content in aragonite promoted by Glu and hexadecanoic acid is more significant. The DFT (density functional theory) calculations reveal that the energy needed for Mg2+ ion incorporation into aragonite mediated by Glu, hexadecanoic acid, Gly and Ala increased gradually, but was lower than that without acidic biomolecules. The experiments also show that the Mg2+ ion content in the aragonite significantly increased with the increasing concentration of biomolecules. In a medium with high Mg2+ concentration and with bacteria, after 2 months, micron-sized dolomite rhombs were precipitated on the surfaces of the aragonite particles. This study may provide new insights into the important role played by biomolecules in the incorporation of the Mg2+ ions into aragonite. Moreover, these experiments may contribute towards our understanding of the dolomitization of aragonite in the presence of bacteria.
Metabolomic profiles of the liquid state fermentation in co-culture of Eurotium amstelodami and Bacillus licheniformis
Authors: Wang Yunsheng , Chen Yincui , Xin Jiankang , Chen Xianjing , Xu Tingyan , He Jiefang , Pan Zhangxu , Zhang Chuanbo
Published: January 2023

As an important source of new drug molecules, secondary metabolites (SMs) produced by microorganisms possess important biological activities, such as antibacterial, anti-inflammatory, and hypoglycemic effects. However, the true potential of microbial synthesis of SMs has not been fully elucidated as the SM gene clusters remain silent under laboratory culture conditions. Herein, we evaluated the inhibitory effect of Staphylococcus aureus by co-culture of Eurotium amstelodami and three Bacillus species, including Bacillus licheniformis, Bacillus subtilis, and Bacillus amyloliquefaciens. In addition, a non-target approach based on ultra-performance liquid chromatography time-of-flight mass spectrometry (UPLC-TOF-MS) was used to detect differences in extracellular and intracellular metabolites. Notably, the co-culture of E. amstelodami and Bacillus spices significantly improved the inhibitory effect against S. aureus, with the combination of E. amstelodami and B. licheniformis showing best performance. Metabolomics data further revealed that the abundant SMs, such as Nummularine B, Lucidenic acid E2, Elatoside G, Aspergillic acid, 4-Hydroxycyclohexylcarboxylic acid, Copaene, and Pipecolic acid were significantly enhanced in co-culture. Intracellularly, the differential metabolites were involved in the metabolism of amino acids, nucleic acids, and glycerophospholipid. Overall, this work demonstrates that the co-culture strategy is beneficial for inducing biosynthesis of active metabolites in E. amstelodami and B. licheniformis.
Therapeutic efficacy of liraglutide versus metformin in modulating the gut microbiota for treating type 2 diabetes mellitus complicated with nonalcoholic fatty liver disease
Authors: Ying Xing , Rongjiong Zheng , Kahaer Mayila , Chunhui Jiang , Wulasihan Muhuyati
Published: January 2023

Metformin and liraglutide are used in the treatment of type 2 diabetes mellitus (T2DM) complicated with nonalcoholic fatty liver disease (NAFLD). Although these drugs can alter the intestinal microbiome, clinical data are required to explore their mechanisms of action. Using 16S sequencing technology, we analyzed and compared the intestinal bacterial community structure and function between patients before and after treatment (12 weeks) with the two drugs (metformin or liraglutide, n = 15) and healthy controls (n = 15). Moreover, combined with 19 clinical indices, the potential therapeutic mechanisms of the two drugs were compared. The studied clinical indices included those associated with islet β-cell function (FPG, FINS, HbA1c, and HOMA-IR), inflammation (TNF-α, IL-6, and APN), lipid metabolism (TC, TG, and LDL-C), and liver function (ALT, AST, and GGT); the values of all indices changed significantly after treatment (p < 0.01). In addition, the effect of the two drugs on the intestinal bacterial community varied. Liraglutide treatment significantly increased the diversity and richness of the intestinal bacterial community (p < 0.05); it significantly increased the relative abundances of Bacteroidetes, Proteobacteria, and Bacilli, whereas metformin treatment significantly increased the relative abundance of Fusobacteria and Actinobacteria (p < 0.05). Metformin treatment increased the complexity and stability of the intestinal bacterial network. However, liraglutide treatment had a weaker effect on the intestinal bacterial network, and the network after treatment was similar to that in healthy controls. Correlation matrix analysis between dominant genera and clinical indicators showed that the correlation between the bacterial community and islet β-cell function was stronger after liraglutide treatment, whereas the correlation between the bacterial community and inflammation-related factors was stronger after metformin treatment. Functional prediction showed that liraglutide could significantly affect the abundance of functional genes related to T2DM and NAFLD (p < 0.05), but the effect of metformin was not significant. This study is the first to report the changes in the intestinal bacterial community in patients treated with metformin or liraglutide and the differences between the mechanisms of action of metformin and liraglutide. Metformin or liraglutide has a therapeutic value in T2DM complicated with NAFLD, with liraglutide having a weaker effect on the intestinal bacterial community but a better therapeutic efficacy.
Advanced treatment of secondary effluent from wastewater treatment plant by a newly isolated microalga Desmodesmus sp. SNN1
Authors: Wang Pengchong , Shao Yahui , Geng Yun , Mushtaq Rubina , Yang Wenlong , Li Mei , Sun Xiuqin , Wang Hongbo , Chen Gao
Published: January 2023

Secondary effluents contain considerable amounts of nitrogen and phosphorous, which if dumped untreated can cause eutrophication of the receiving water bodies. Microalgae can remove these nutrients and other pollutants from the wastewater effluents and play an effective role in the secondary effluent treatment. In this study, six microalgae strains (SNN1, SNN2, SNN3, SNN4, SNS1, and SNS2) were isolated and screened from the water and mud of Yingxue Lake of Shandong Jianzhu University, and their efficiencies for the removal of COD, NH4+-N, TN, and TP in the secondary effluent were assessed. By comparing the growth performances and nutrient removal ability of algal strains in domestic sewage, we found that SNN1 (identified and named as Desmodesmus sp. SNN1) has the highest efficiency for biomass accumulation and sewage purification. Hence, the algal strain SNN1 was selected for further screening and optimization experiments. The strain showed higher biomass yield and better nutrient removal rate when the pH of secondary effluent was 9.0 and the initial inoculum concentration (optical density at 680 nm) of algal strain was 0.4. After 12 days of treatment, the concentrations of COD, NH4+-N, TN, and TP in the secondary effluent were 31.79, 0.008, 8.631, and 0.069 mg/L, respectively. Therefore, SNN1 with the removal rates of 52.69% (COD), 99.99% (NH4+-N), 89.09% (TN), and 94.64% (TP) displayed its high potential in nutrient removal. In addition, it also yielded 5.30 mg/L of chlorophyll a and 168.33 mg/L of lipids. These results demonstrated that this strain exhibited an effective treatment capacity for secondary effluent and microalgal oil production. This study is helpful to provide a strategy for the resource utilization of secondary effluent and the conservation of freshwater resources required by microalgae culture.
Clomazone impact on fungal network complexity and stability
Authors: He Hairong , Huang Jiarui , Zhao Zhenzhu , Feng Weisheng , Zheng Xiaoke , Du Pengqiang
Published: January 2023

Introduction

Soil fungal network composition and stability are important for soil functions, but there is less understanding of the impact of clomazone on network complexity and stability.

Methods

In this work, two agricultural soils were used to investigate the impact of clomazone on fungal network complexity, composition, and stability. The two soils were treated with clomazone solution (0, 0.8, 8, and 80  mg kg−1) and kept in an incubator.

Results and Discussion

Under the influence of clomazone, the fungal network nodes were decreased by 12–42; however, the average degree was increased by 0.169–1.468 and fungal network density was increased by 0.003–0.054. The keystone nodes were significantly changed after clomazone treatment. Network composition was also impacted. Specifically, compared with control and clomazone treatments in both soils, the shared edges were fewer than 54 in all comparisons, and network dissimilarity was 0.97–0.98. These results suggested that fungal network composition was significantly impacted. The network robustness was increased by 0.0018–0.0209, and vulnerability was decreased by 0.00018–0.00059 in both soils, which indicated that fungal network stability was increased by clomazone. In addition, the functions of network communities were also changed in both soils. These results indicated that clomazone could significantly impact soil fungal networks.
The Evolution of Intein-Based Affinity Methods as Reflected in 30 years of Patent History
Authors: Prabhala Sai Vivek , Gierach Izabela , Wood David W.
Published: January 2023

Self-cleaving affinity tags, based on engineered intein protein domains, have been touted as a universal single step purification platform for tagless non-mAb proteins. These approaches provide all of the power and flexibility of tag-based affinity methods, but deliver a tagless target protein suitable for clinical applications without complex process development. This combination of features might accelerate and de-risk biopharmaceutical development by bridging early discovery to full-scale manufacturing under a single platform. Despite this profound promise, intein-based technologies have yet to reach their full potential. This review examines the evolution of intein-based purification methods in the light of several significant intein patents filed over the last 3 decades. Illustrated with actual key figures from each of the relevant patents, key advances are described with a focus on applications in basic research and biopharmaceutical production. Suggestions for extending intein-based purification systems to emerging therapies and non-protein applications are presented as concluding remarks.
Structure of co-expression networks of Bifidobacterium species in response to human milk oligosaccharides
Authors: González-Morelo Kevin J. , Galán-Vásquez Edgardo , Melis Felipe , Pérez-Rueda Ernesto , Garrido Daniel
Published: January 2023

Biological systems respond to environmental perturbations and a large diversity of compounds through gene interactions, and these genetic factors comprise complex networks. Experimental information from transcriptomic studies has allowed the identification of gene networks that contribute to our understanding of microbial adaptations. In this study, we analyzed the gene co-expression networks of three Bifidobacterium species in response to different types of human milk oligosaccharides (HMO) using weighted gene co-expression analysis (WGCNA). RNA-seq data obtained from Geo Datasets were obtained for Bifidobacterium longum subsp. Infantis, Bifidobacterium bifidum and Bifidobacterium longum subsp. Longum. Between 10 and 20 co-expressing modules were obtained for each dataset. HMO-associated genes appeared in the modules with more genes for B. infantis and B. bifidum, in contrast with B. longum. Hub genes were identified in each module, and in general they participated in conserved essential processes. Certain modules were differentially enriched with LacI-like transcription factors, and others with certain metabolic pathways such as the biosynthesis of secondary metabolites. The three Bifidobacterium transcriptomes showed distinct regulation patterns for HMO utilization. HMO-associated genes in B. infantis co-expressed in two modules according to their participation in galactose or N-Acetylglucosamine utilization. Instead, B. bifidum showed a less structured co-expression of genes participating in HMO utilization. Finally, this category of genes in B. longum clustered in a small module, indicating a lack of co-expression with main cell processes and suggesting a recent acquisition. This study highlights distinct co-expression architectures in these bifidobacterial genomes during HMO consumption, and contributes to understanding gene regulation and co-expression in these species of the gut microbiome.
Extensive accumulation of misfolded protein aggregates during natural aging and senescence
Authors: Cuanalo-Contreras Karina , Schulz Jonathan , Mukherjee Abhisek , Park Kyung-Won , Armijo Enrique , Soto Claudio
Published: January 2023

Accumulation of misfolded protein aggregates is a hallmark event in many age-related protein misfolding disorders, including some of the most prevalent and insidious neurodegenerative diseases. Misfolded protein aggregates produce progressive cell damage, organ dysfunction, and clinical changes, which are common also in natural aging. Thus, we hypothesized that aging is associated to the widespread and progressive misfolding and aggregation of many proteins in various tissues. In this study, we analyzed whether proteins misfold, aggregate, and accumulate during normal aging in three different biological systems, namely senescent cells, Caenorhabditis elegans, and mouse tissues collected at different times from youth to old age. Our results show a significant accumulation of misfolded protein aggregates in aged samples as compared to young materials. Indeed, aged samples have between 1.3 and 2.5-fold (depending on the biological system) higher amount of insoluble proteins than young samples. These insoluble proteins exhibit the typical characteristics of disease-associated aggregates, including insolubility in detergents, protease resistance, and staining with amyloid-binding dye as well as accumulation in aggresomes. We identified the main proteins accumulating in the aging brain using proteomic studies. These results show that the aged brain contain large amounts of misfolded and likely non-functional species of many proteins, whose soluble versions participate in cellular pathways that play fundamental roles in preserving basic functions, such as protein quality control, synapsis, and metabolism. Our findings reveal a putative role for protein misfolding and aggregation in aging.
Optimizing the mnemonic similarity task for efficient, widespread use
Authors: Stark Craig E. L. , Noche Jessica A. , Ebersberger Jarrett R. , Mayer Lizabeth , Stark Shauna M.
Published: January 2023

Introduction: The Mnemonic Similarity Task (MST) has become a popular test of memory and, in particular, of hippocampal function. It has been heavily used in research settings and is currently included as an alternate outcome measure on a number of clinical trials. However, as it typically requires ~15 min to administer and benefits substantially from an experienced test administrator to ensure the instructions are well-understood, its use in trials and in other settings is somewhat restricted. Several different variants of the MST are in common use that alter the task format (study-test vs. continuous) and the response prompt given to participants (old/similar/new vs. old/new).

Methods: In eight online experiments, we sought to address three main goals: (1) To determine whether a robust version of the task could be created that could be conducted in half the traditional time; (2) To determine whether the test format or response prompt choice significantly impacted the MST’s results; and (3) To determine how robust the MST is to repeat testing. In Experiments 1–7, participants received both the traditional and alternate forms of the MST to determine how well the alternate version captured the traditional task’s performance. In Experiment 8, participants were given the MST four times over approximately 4 weeks.

Results: In Experiments 1–7, we found that test format had no effect on the reliability of the MST, but that shifting to the two-choice response format significantly reduced its ability to reflect the traditional MST’s score. We also found that the full running time could be cut it half or less without appreciable reduction in reliability. We confirmed the efficacy of this reduced task in older adults as well. Here, and in Experiment 8, we found that while there often are no effects of repeat-testing, small effects are possible, but appear limited to the initial testing session.

Discussion: The optimized version of the task developed here (oMST) is freely available for web-based experiment delivery and provides an accurate estimate of the same memory ability as the classic MST in less than half the time.
Preadolescent exposure to a sexually mature, unrelated male rat reduces postadolescent social recognition memory and CA2 c-Fos labeling
Authors: Maletta Teresa , Palummieri Michael , Correa Jeff , Holahan Matthew R.
Published: January 2023

Introduction

Social memory involves social recognition: the ability to discriminate between two or more conspecifics when one has been previously encountered. The CA2 region of the hippocampus has been implicated in social memory, as lesions and dysfunction to this area lead to social memory impairments. A variety of psychogenic manipulations during postnatal sensitive developmental periods are associated with social memory impairments later in life.

Methods

In this study, we exposed preadolescent rats to a sexually, mature unrelated male and examined whether this was associated with changes in postadolescent social memory and c-Fos labeling in the CA2 region. Male and female Long-Evans rats were exposed to a male, adult rat on postnatal days 19–21 (P19–21). Social memory was measured during the postadolescent period and defined as increased interactions towards a novel age-matched rat in contrast to a previously-encountered age-matched rat. After the test, rats were euthanized and brain tissue was then collected to quantify c-Fos labeling within the CA2 region.

Results

Compared to home cage controls and controls not exposed to the adult male, male and female rats exposed to the unrelated adult during preadolescence were unable to discriminate between a novel and previously encountered conspecific during the postadolescent test showing social memory deficits. The groups that showed social recognition deficits also had significantly fewer c-Fos-positive cells within the CA2 region compared to the control groups.

Discussion

These findings indicate that threatening psychogenic encounters during preadolescence can have detrimental long-term effects on social memory potentially via disrupted activity in the CA2 hippocampal region.
Dual role of Apolipoprotein D as long-term instructive factor and acute signal conditioning microglial secretory and phagocytic responses
Authors: Corraliza-Gomez Miriam , Bendito Beatriz , Sandonis-Camarero David , Mondejar-Duran Jorge , Villa Miguel , Poncela Marta , Valero Jorge , Sanchez Diego , Ganfornina Maria D.
Published: January 2023

Microglial cells are recognized as very dynamic brain cells, screening the environment and sensitive to signals from all other cell types in health and disease. Apolipoprotein D (ApoD), a lipid-binding protein of the Lipocalin family, is required for nervous system optimal function and proper development and maintenance of key neural structures. ApoD has a cell and state-dependent expression in the healthy nervous system, and increases its expression upon aging, damage or neurodegeneration. An extensive overlap exists between processes where ApoD is involved and those where microglia have an active role. However, no study has analyzed the role of ApoD in microglial responses. In this work, we test the hypothesis that ApoD, as an extracellular signal, participates in the intercellular crosstalk sensed by microglia and impacts their responses upon physiological aging or damaging conditions. We find that a significant proportion of ApoD-dependent aging transcriptome are microglia-specific genes, and show that lack of ApoD in vivo dysregulates microglial density in mouse hippocampus in an age-dependent manner. Murine BV2 and primary microglia do not express ApoD, but it can be internalized and targeted to lysosomes, where unlike other cell types it is transiently present. Cytokine secretion profiles and myelin phagocytosis reveal that ApoD has both long-term pre-conditioning effects on microglia as well as acute effects on these microglial immune functions, without significant modification of cell survival. ApoD-triggered cytokine signatures are stimuli (paraquat vs. Aβ oligomers) and sex-dependent. Acute exposure to ApoD induces microglia to switch from their resting state to a secretory and less phagocytic phenotype, while long-term absence of ApoD leads to attenuated cytokine induction and increased myelin uptake, supporting a role for ApoD as priming or immune training factor. This knowledge should help to advance our understanding of the complex responses of microglia during aging and neurodegeneration, where signals received along our lifespan are combined with damage-triggered acute signals, conditioning both beneficial roles and limitations of microglial functions.
Sex differences and risk factors in recurrent ischemic stroke
Authors: Chung Ji Yeon , Lee Bit Na , Kim Young Seo , Shin Byoung-Soo , Kang Hyun Goo
Published: January 2023

Introduction

Recurrent ischemic stroke (RIS) is associated with increased mortality and poor outcomes. Therefore, secondary prevention is critical for reducing the risk of recurrent stroke. Previous studies have found sex differences in risk factors in patients with first-ever stroke; however, the results have been inconsistent for recurrent stroke. Therefore, this study aimed to investigate whether there are significant sex differences in the clinical characteristics and risk factors for recurrent ischemic stroke.

Methods

We retrospectively studied 787 patients with recurrent ischemic stroke after first-ever stroke confirmation using magnetic resonance imaging (MRI) after visiting a regional tertiary hospital between 2014 and 2020. Demographic characteristics, laboratory findings, and risk factors were compared between the male and female patients. In addition, multivariate logistic regression was performed to identify the independent factors associated with stroke recurrence in male patients.

Results

Among the 787 patients, 466 (59.2%) were males. Males were younger than females (67.6 vs. 71.9 years). Females had higher rates of hypertension, diabetes mellitus, dyslipidemia, and overweight than those of males. However, the alcohol drinking and smoking rate were significantly higher in males than that in females. There were no statistically significant sex-based differences in the laboratory findings. Among males, hypertension, alcohol drinking, smoking and dyslipidemia was a significant risk factor for ischemic stroke recurrence.

Conclusion

Hypertension and dyslipidemia were significant risk factors of recurrent ischemic stroke in both genders. Smoking and alcohol drinking were significant risk factors associated with ischemic stroke recurrence in males. Therefore, smoking cessation and alcohol abstinence are recommended after the first stroke to prevent recurrent ischemic stroke especially for males. Diabetes was a significant risk factor of ischemic stroke recurrence in females. More extensive studies are needed to understand the causal relationship of each factors with ischemic stroke recurrence according to sex differences and specification of preventive management is needed.
The differences of orthostatic hypotension in patients with Parkinson's disease and multiple system atrophy
Authors: Zeng Jingrong , Xing Yingqi , Mei Shanshan , Xu Baolei , Xue Xiaofan , Song Haixia , Xu Erhe
Published: January 2023

Background

Multiple system atrophy (MSA) and Parkinson's disease (PD) have similar clinical presentations in their early stages. Orthostatic hypotension (OH) is a common autonomic dysfunction associated with MSA and PD. Heart rate (HR) and systolic blood pressure (SBP) changes are measured in response to the active standing test, which is widely used to screen for cardiovascular autonomic function.

Objectives and methods

Overall, 255 patients (67 MSA, 188 PD) underwent continuous beat-to-beat non-invasive BP monitoring and active standing test. The total standing time was 10 min, and the BP differences between both groups were compared to determine whether the ΔHR/ΔSBP can differentiate both conditions.

Results

Classical orthostatic hypotension (COH) (52%) and initial OH (19%) were most common in MSA and PD, respectively. MSA had a higher HR (75.0 ± 9.7 vs. 71.0 ± 10.7, P = 0.008) than PD in the supine position. SBP (135.70 ± 15.68 mmHg vs. 127.31 ± 15.14 mmHg, P = 0.106), diastolic BP (78.45 ± 12.36 mmHg vs. 67.15 ± 13.39 mmHg, P = 0.009) and HR (73.94 ± 8.39 bpm vs. 71.08 ± 13.52 bpm, P = 0.389) at baseline were higher in MSA-COH than in PD-COH. After adjusting for age and disease duration, the ΔHR/ΔSBP-10 min significantly discriminated MSA-COH from PD-COH (P = 0.031). An ΔHR/ΔSBP-10 min of 0.517 showed a sensitivity of 67% and specificity of 84% (AUC = 0.77, 95% CI: 0.63–0.91).

Conclusion

The SBP, diastolic BP, and HR were higher in the supine position; however, ΔHR and ΔSBP were lower after standing in MSA patients than in PD patients. The ΔHR/ΔSBP-10 min discriminated between MSA-COH and PD-COH with quiet acceptable accuracy.