bluuebunny/crossref_metadata_2025 huggingface dataset:
Analyzing the pathogenesis of systemic lupus erythematosus complicated by atherosclerosis using transcriptome data
Authors: Wang Yimin , Su Wenge , Li Yunlun , Yuan Jie , Yao Minghao , Su Xiaoyi , Wang Yifei
Published: July 2022

Background

Accumulating evidence supports the predisposition of systemic lupus erythematosus (SLE) to atherosclerosis (AS). However, the common pathogenesis of these two diseases remains unclear. This study aimed to explore the mechanisms of SLE complicated by AS.

Methods

Gene expression profiles of SLE (GSE50772) and AS (GSE100927) were downloaded from the Gene Expression Omnibus. We analyzed differentially expressed genes (DEGs) of SLE and AS and performed enrichment analyses separately. After analyzing the common DEGs (CDEGs), we performed functional enrichment analysis, protein-protein interaction (PPI) network analysis, and hub genes (HGs) identification of CDEGs. Then, we performed a co-expression analysis of HGs and verified their expression and diagnostic value. We further explored immune cell infiltration and analyzed the correlation between HGs and infiltrating immune cells (IICs). Finally, we verified the reliability of the screening pathway.

Results

We obtained 530 DEGs from the GSE50772 dataset and 448 DEGs from the GSE100927 dataset. The results of the enrichment analysis showed that there were many similar immune- and inflammation-related processes between the two diseases. We analyzed 26 CDEGs (two downregulated genes and 24 upregulated genes) and enrichment analysis highlighted the important role of the IL-17 signaling pathway. We identified five HGs (CCR1, CD163, IL1RN, MMP9, and SIGLEC1) using the CytoHubba plugin and HGs validation showed that the five HGs screened were reliable. Co-expression networks showed that five HGs can affect mononuclear cell migration. Immune cell infiltration analysis indicated monocytes in SLE and M0 macrophages in AS accounted for a high proportion of all IICs, and the difference in infiltration was obvious. We also found a significant positive correlation between CCR1, CD163, IL1RN, and MMP9 and monocytes in SLE, and a significant positive correlation between CCR1, IL1RN, MMP9, and SIGLEC1 and M0 macrophages in AS. Pathway validation also demonstrated that the IL-17 signaling pathway was a key pathway for the differentiation of monocytes into macrophages.

Conclusions

The five HGs may promote the differentiation of monocytes into macrophages by influencing the IL-17 signaling pathway, leading to SLE complicated by AS. Our study provides insights into the mechanisms of SLE complicated by AS.
Pretransplant characteristics of kidney transplant recipients that predict posttransplant outcome
Authors: Tepel Martin , Nagarajah Subagini , Saleh Qais , Thaunat Olivier , Bakker Stephan J. L. , van den Born Jacob , Karsdal Morten A. , Genovese Federica , Rasmussen Daniel G. K.
Published: July 2022

Better characterization of the potential kidney transplant recipient using novel biomarkers, for example, pretransplant plasma endotrophin, will lead to improved outcome after transplantation. This mini-review will focus on current knowledge about pretransplant recipients’ characteristics, biomarkers, and immunology. Clinical characteristics of recipients including age, obesity, blood pressure, comorbidities, and estimated survival scores have been introduced for prediction of recipient and allograft survival. The pretransplant immunologic risk assessment include histocompatibility leukocyte antigens (HLAs), anti-HLA donor-specific antibodies, HLA-DQ mismatch, and non-HLA antibodies. Recently, there has been the hope that pretransplant determination of markers can further improve the prediction of posttransplant complications, both short-term and long-term outcomes including rejections, allograft loss, and mortality. Higher pretransplant plasma endotrophin levels were independently associated with posttransplant acute allograft injury in three prospective European cohorts. Elevated numbers of non-synonymous single-nucleotide polymorphism mismatch have been associated with increased allograft loss in a multivariable analysis. It is concluded that there is a need for integration of clinical characteristics and novel molecular and immunological markers to improve future transplant medicine to reach better diagnostic decisions tailored to the individual patient.
Puerarin ameliorates nonalcoholic fatty liver in rats by regulating hepatic lipid accumulation, oxidative stress, and inflammation
Authors: Zhou Jingxuan , Zhang Nanhai , Aldhahrani Adil , Soliman Mohamed Mohamed , Zhang Liebing , Zhou Feng
Published: July 2022

Nonalcoholic fatty liver disease (NAFLD) has become one of the public health problems globally. The occurrence of NAFLD is usually accompanied by a series of chronic metabolic diseases, with a prevalence rate is 25.24% among adults worldwide. Therefore, NAFLD seriously affects the quality of life in patients and causes a large economic burden. It has been reported that puerarin has the function of lowering the serum lipids, but due to the complexity of NAFLD, the specific mechanism of action has not been clarified. The aim of this study was to evaluate the preventive or ameliorating effects of two doses of puerarin (0.11% and 0.22% in diet) on high-fat and high-fructose diet (HFFD)-induced NAFLD in rats. The rats were fed with HFFD-mixed puerarin for 20 weeks. The results showed that puerarin ameliorated the levels of lipids in the serum and liver. Further exploration of the mechanism found that puerarin ameliorated hepatic lipid accumulation in NAFLD rats by reducing the expression of Srebf1, Chrebp, Acaca, Scd1, Fasn, Acacb, Cd36, Fatp5, Degs1, Plin2, and Apob100 and upregulating the expression of Mttp, Cpt1a, and Pnpla2. At the same time, after administration of puerarin, the levels of antioxidant markers (superoxide dismutase, glutathione peroxidase, and catalase) were significantly increased in the serum and liver, and the contents of serum and hepatic inflammatory factors (interleukin-18, interleukins-1β, and tumor necrosis factor α) were clearly decreased. In addition, puerarin could ameliorate the liver function. Overall, puerarin ameliorated HFFD-induced NAFLD by modulating liver lipid accumulation, liver function, oxidative stress, and inflammation.
Drug development for onchocerciasis-the past, the present and the future
Authors: Tagboto Senyo , Orish Verner
Published: July 2022

Onchocerciasis affects predominantly rural communities in Africa, and with small foci in South America and the Yemen. The disease is a major cause of blindness and other significant morbidity and mortality. Control programs have achieved a major impact on the incidence and prevalence of onchocerciasis by interrupting transmission with vector control programs, and treatment with mass drug administration using the microfilaricide ivermectin. Over the last few decades, several microfilaricides have been developed. This initially included diethylcarbamazine, which had significant side effects and is no longer used as such. Ivermectin which is a safe and highly effective microfilaricide and moxidectin which is a longer acting microfilaricide are presently recognized therapies. Suramin was the first effective macrofilaricide but was prohibitively toxic. Certain antibiotics including doxycycline can help eliminate adult worms by targeting its endosymbiont bacteria, Wolbachia pipientis. However, the dosing regimens may make this difficult to use as part of a mass disease control program in endemic areas. It is now widely recognized that treatments that are able to kill or permanently sterilize adult filarial worms should help achieve the elimination of this disease. We summarize in detail the historic drug development in onchocerciasis, including prospective future candidate drugs.
Elevated pCO2 Induced Physiological, Molecular and Metabolic Changes in Nannochloropsis Oceanica and Its Effects on Trophic Transfer
Authors: Liang Chengwei , Zhang Yufei , Gu Zipeng , Ren Yudong , Zhang Xiaowen , Xu Dong , Ye Naihao
Published: July 2022

The rise of dissolution of anthropogenic CO2 into the ocean alters marine carbonate chemistry and then results in ocean acidification (OA). It has been observed that OA induced different effects on different microalgae. In this study, we explored the physiological and biochemical changes in Nannochloropsis oceanica in response to increased atmospheric carbon dioxide and tested the effect of ocean acidification (OA) on the food web through animal feeding experiments at a laboratory scale. We found that the levels of C, N, C/N, Fv/Fm, and photosynthetic carbon fixation rate of algae cells were increased under high carbon dioxide concentration. Under short-term acidification, soluble carbohydrate, protein, and proportion of unsaturated fatty acids in cells were significantly increased. Under long-term acidification, the proportion of polyunsaturated fatty acids (PUFAs) (~33.83%) increased compared with that in control (~30.89%), but total protein decreased significantly compared with the control. Transcriptome and metabonomics analysis showed that the differential expression of genes in some metabolic pathways was not significant in short-term acidification, but most genes in the Calvin cycle were significantly downregulated. Under long-term acidification, the Calvin cycle, fatty acid biosynthesis, TAG synthesis, and nitrogen assimilation pathways were significantly downregulated, but the fatty acid β-oxidation pathway was significantly upregulated. Metabolome results showed that under long-term acidification, the levels of some amino acids increased significantly, while carbohydrates decreased, and the proportion of PUFAs increased. The rotifer Brachionus plicatilis grew slowly when fed on N. oceanica grown under short and long-term acidification conditions, and fatty acid profile analysis indicated that eicosapentaenoic acid (EPA) levels increased significantly under long-term acidification in both N. oceanica (~9.48%) and its consumer B. Plicatilis (~27.67%). It can be seen that N. oceanica formed a specific adaptation mechanism to OA by regulating carbon and nitrogen metabolism, and at the same time caused changes of cellular metabolic components. Although PUFAs were increased, they still had adverse effects on downstream consumers.
Microplastics in commercial clams from the intertidal zone of the South Yellow Sea, China
Authors: Tang Ruikai , Zhang Tao , Song Kexin , Sun Yixin , Chen Yangjun , Huang Wei , Feng Zhihua
Published: July 2022

Clams are commercially important species and are a vital component of the offshore ecosystem. Investigations on microplastics (MPs) in clams have attracted public attention recently, for its ecological and food safety risks. However, knowledge gaps still exist regarding MPs in commercial clams from the intertidal zone of the South Yellow Sea (SYS), China, an important clam habitat. In this study, to investigate the distribution of MPs in clams of the SYS, four species of clams were collected from nine sites in different tide zones (high, middle, and low tides) in three coastal areas (Nantong, Yancheng and Lianyungang). The abundance and characteristics of MPs, including size, shape, color and composition, were determined using microscope and micro-Fourier transform infrared (FTIR) spectroscopy. Furthermore, to evaluate the MPs purification ability of clams, the abundance of MPs in various tissues was examined by microscopic observation after being purified in filtered seawater for 72 h. The results showed that there were significant differences in the abundance of MPs in clams from different regions, with the most serious pollution in the high-tide zone. Moreover, the lowest MPs abundance was found in Yancheng (5.07 ± 2.73 items/individual, 1.16 ± 0.78 items/g), while Lianyungang was found with the most abundant MPs (7.52 ± 2.68 items/individual, 3.94 ± 3.00 items/g). The size of MPs in Ruditapes philippinarum (1,329.99 μm) was significantly higher than in other species. The MPs in clams were characterized by fiber in shape, black-grey, blue-green and white-transparent in color and rayon in composition. Moreover, it was found that the MPs originally present in various tissues tended to migrate and accumulate into the mantle of the clam during depuration, and after 72 h of depuration, removing the mantle could reduce nearly half amount of microplastics in clams. Overall, our study revealed the microplastic distribution in commercial clams from the intertidal zone of the SYS and provided suggestions for the safety of aquatic production.
Impact of Typhoon on Coastal Upwelling Off The Eastern Hainan Island: A Case Study of Typhoon Rammasun (2014)
Authors: Hong Bo , Huang Xiongxing , Liu Sumin , Xu Hongzhou
Published: July 2022

The Hainan Island coastal upwelling (HIU hereafter) off the eastern Hainan Island (EHI) is an important phenomenon in the northern South China Sea. Though this phenomenon has been extensively studied, the fast responses of its inner oceanic processes to typhoon passage remain unclear. Based on satellite data and a validated three-dimensional numerical model, the HIU response to the passage of Typhoon Rammasun (2014) are explored in this study. Impacted by Rammasun, the climbing of deep water off the EHI was depressed and the bottom cold water moved seaward for at least 10 km. Though the HIU was weakened, a cooling event and Chl-a bloom in the HIU were formed after the passage of Rammasun. Diagnostic analyses revealed that both advection and diffusion terms contributed to controlling the local rate of temperate change during the typhoon passage and the advection terms showed significant internal wave signals along the shelf break off southeastern Hainan Island. At the same time, strong near-inertial waves (NIWs) with 0.705 cpd were triggered in the HIU. The NIWs lasted for about two weeks and caused strong vertical mixing in the HIU after Rammasun. Overall, typhoon wind and NIWs combined to dominate temperature variation in the HIU during the typhoon period.
Modelling the Role of Temperature-Induced Environmental Noise on Phytoplankton Niche Dynamics
Authors: Sarker Subrata , Mohammad Deen , Nabil Siam Ahmed , Kabir Md. Alamgir
Published: July 2022

Variability in physical and chemical processes in the marine ecosystem significantly influences the niche ecology of primary producers. However, studies are limited to understand the role of variability in environmental conditions on the niche dynamics of phytoplankton. Therefore, in this study we aimed to understand the role of environmental noise on the niche dynamics of phytoplankton species. This study performed numerical simulations by extending the classic Rosenzweig–MacArthur, predator–prey model for multiple species. We considered the characteristics timescale of seasonal sea surface temperature as environmental noise. Our study found that the oscillatory fluctuation of biomass, variation in carrying capacity, no competitive exclusion, and non-equilibrium state in periodic fluctuation of species biomass enables species to coexist in a noise-induced system. In addition, a high amplitude in species biomass fluctuation at a higher environmental noise was found as another potential coexistence mechanism. Our simulations found that the mean niche and niche width of species are significantly related to environmental noise (R2 = 0.93 and 0.98, respectively). We observed a shift in mean niche conditions of species with the change in environmental noise. Niche overlapping between species decreased significantly with the increase in environmental noise (R2 = 0.95). Our study will serve as a baseline to understand the complexity of phytoplankton niche dynamics in a variable environment.
The Impact of Climate Change on Bivalve Farming: Combined Effect of Temperature and Salinity on Survival and Feeding Behavior of Clams Ruditapes decussatus
Authors: Rato Ana , Joaquim Sandra , Matias Ana Margarete , Roque Cláudia , Marques António , Matias Domitília
Published: July 2022

European clam (Ruditapes decussatus) is one of the most relevant emergent bivalve species from the aquaculture sector in Europe with high economic value. Climate changes represent a potential limiting factor to this activity, directly interfering with the survival and behavior of bivalves. Severe fluctuations in temperature along with periods of heavy rainfall or periods of drought that significantly change the salinity can promote physiological stress in bivalves, resulting in changes in physiological and behavioral responses and, in extreme cases, leading to high mortalities. This study aimed to evaluate the combined effect of temperature and salinity on mortality and feeding behavior of R. decussatus. Juveniles and adults were exposed to combined ranges of temperature (5°C–35°C) and salinity (0–40). Mortality and feeding behavior were registered every 24 h of each 120-h trial. A control temperature range was set between 15°C and 23°C, where mortality and feeding behavior were considered as the normal scenario. Our data suggested salinity 15 as a “turning point,” a point from which occurred distinct patterns in mortality and feeding behavior. The results evidently indicate that abrupt reductions in salinity and sharp increases in temperature will lead to high mortality of R. decussatus. Juveniles were revealed to be more sensitive to the increase of temperature in a less saline environment, to suffer greater and faster mortalities, and to be more resistant to extremely high temperatures under more saline conditions. The high temperatures and sporadic heavy rainfall that are predicted to occur in the south of Europe due to climate changes will contribute to compromise the recruitment of European clam, thus threatening the production of this species and consequently impacting the economic sector.
Closed life-cycle aquaculture of sea lettuce (Ulva fenestrata): performance and biochemical profile differ in early developmental stages
Authors: Steinhagen Sophie , Larsson Karin , Olsson Joakim , Albers Eva , Undeland Ingrid , Pavia Henrik , Toth Gunilla B.
Published: July 2022

Sea lettuce (Ulva) aquaculture has increased the last decade due to high productivity, wide environmental tolerance, and interesting functional and nutritional properties of the crop. Research focus has mainly been on adult biomass production, but knowledge of performance and biochemical content of early developmental stages – which are the basis to any large-scale production - is still limited. The life-history ofUlvaalternates between a diploid sporophytic life-stage and a haplontic gametophytic life-stage. Whereas the sporophyte give raise to recombinant gametophytes through zoids, gametophytes can give raise to parthenogenetically developing, clonal gametes in absence of a mating partner. This study shows that recombinant gametophytes have a faster ontogenetic development, higher growth rate, as well as higher protein, fatty acid, and pigment contents compared to clonal gametophytes of the cropUlva fenestrata. Nutrient addition is required for a normal development, but temperature and swarmer density have relatively small effects on the hatchery success, relative growth rate and biochemical profile of the juvenile biomass. Our study reveals that the selection of the life-history-phase in novel sea lettuce crop strains could largely contribute to the emerging seaweed aquaculture sector.
Synergistic effect of microneedle-delivered extracellular matrix compound and radiofrequency on rejuvenation of periorbital wrinkles
Authors: Cheng Haiyan , Zhang Ruina , Zhuo Fenglin
Published: July 2022

Background

A combination of minimally invasive modalities can induce collagen regeneration more quickly and promote the penetration of topical agents, thus promoting skin rejuvenation. In this study, we aimed to investigate the synergistic efficacy of extracellular matrix compound (ECM-C) via microneedle (MN) and radiofrequency (RF) on periorbital wrinkles.

Method

A total of 25 participants with periorbital wrinkles were selected for this study. The left and right side of the periorbital area was randomly given ECM-C via MN or ECM-C via MN combined with RF. MN combined with ECM-C treatment was given 5 times at 2 weeks intervals, whereas RF treatment was given 3 times at 4-week intervals. The following items were assessed: wrinkles by VISIA® system; biophysical parameters such as skin hydration, transepidermal water loss (TEWL), erythema index, and melanin index by CK multiple probe adapter; and skin elasticity and skin thickness by DermaLab Combo® photographs were taken at the baseline and 2 weeks after the last treatment. Subjective assessments, such as Crow's Feet Grading Scale (CFGS) and Global Aesthetic International Scale (GAIS), were also recorded.

Result

A total of 25 participants with an average age of 43 years participated in this trial. Periorbital wrinkles on both sides decreased after the treatment, and the side treated with ECM via MN and RF showed better improvement than the other side with ECM-C via MN alone. Skin hydration increased after the treatment on both sides. TEWL, skin erythema, and skin melanin indexes were not changed. Skin elasticity and skin thickness increased more on the side of ECM-C via MN and RF than on the other side of ECM-C via MN alone. The evaluation scores for CFGS improved on either side; however, no difference was found for CFGS and GAIS between intergroup comparisons after the treatment.

Conclusion

The objective assessment of wrinkles, elasticity, and thickness of periorbital skin improved more on the side with ECM-C treatment via MN combined with RF than on the other side of ECM-C treatment via MN only. However, no statistically significant difference was found between the subjective CFGS and GAIS evaluation of the two sides.
Endometriosis and irritable bowel syndrome: A systematic review and meta-analyses
Authors: Nabi Michelle Y. , Nauhria Samal , Reel Morgan , Londono Simon , Vasireddi Anisha , Elmiry Mina , Ramdass Prakash V. A. K.
Published: July 2022

Objective

To estimate the pooled odds ratio of endometriosis and irritable bowel syndrome, and to estimate the pooled prevalence of irritable bowel syndrome in patients with endometriosis.

Data sources

Using Cochrane Library, MEDLINE, Science Direct, ClinicalTrials.gov, Web of Science, and CINAHL, we conducted a systematic literature search through October 2021, using the key terms “endometriosis” and “irritable bowel syndrome.” Articles had to be published in English or Spanish. No restriction on geographical location was applied.

Methods of study selection

The following eligibility criteria were applied: full-text original articles; human studies; studies that investigated the association between endometriosis and irritable bowel syndrome. Two investigators screened and reviewed the studies. A total of 1,776 studies were identified in 6 separate databases. After screening and applying the eligibility criteria, a total of 17 studies were included for analyses. The meta-analysis of association between endometriosis and irritable bowel syndrome included 11 studies, and the meta-analysis on the prevalence of irritable bowel syndrome in endometriosis included 6 studies.

Tabulation, integration, and results

Overall 96,119 subjects were included in the main meta-analysis (11 studies) for endometriosis and irritable bowel syndrome, with 18,887 endometriosis patients and 77,171 controls. The odds of irritable bowel syndrome were approximately 3 times higher among patients with endometriosis compared with healthy controls (odds ratio 2.97; 95% confidence interval, 2.17 – 4.06). Similar results were obtained after subgroup analyses by endometriosis diagnosis, irritable bowel syndrome diagnostic criteria, and Newcastle-Ottawa Scale scores. Six studies reported prevalence rates of irritable bowel syndrome in women with endometriosis, ranging from 10.6 to 52%. The pooled prevalence of irritable bowel syndrome in women with endometriosis was 23.4% (95% confidence interval, 9.7 – 37.2).

Conclusion

Patients with endometriosis have an approximately threefold increased risk of developing irritable bowel syndrome. Development and recent update of Rome criteria has evolved the diagnosis of IBS, potential bias should still be considered as there are no specific tests available for diagnosis.

Systematic Review Registration

[https://www.crd.york.ac.uk/prospero/displa y_record.php?ID=CRD42018080611], identifier [CRD42018080611].
Three-Month Follow-Up of Heterologous vs. Homologous Third SARS-CoV-2 Vaccination in Kidney Transplant Recipients: Secondary Analysis of a Randomized Controlled Trial
Authors: Heinzel Andreas , Schrezenmeier Eva , Regele Florina , Hu Karin , Raab Lukas , Eder Michael , Aigner Christof , Jabbour Rhea , Aschauer Constantin , Stefanski Ana-Luisa , Dörner Thomas , Budde Klemens , Reindl-Schwaighofer Roman , Oberbauer Rainer
Published: July 2022

Response to SARS-CoV-2-vaccines in kidney-transplant recipients (KTR) is severely reduced. Heterologous3rd vaccination combining mRNA and vector vaccines did not increase seroconversion at 4 weeks after vaccination, but evolution of antibody levels beyond the first month remains unknown. We have recently completed a randomized-controlled trial on heterologous (Ad26COVS1) vs. homologous (BNT162b2 or mRNA-1273) 3rd vaccination in 201 KTR not developing SARS-CoV-2-spike-protein antibodies following two doses of mRNA vaccine (EurdraCT: 2021-002927-39). Here, we report seroconversion at the second follow-up at 3 months after the 3rd vaccination (prespecified secondary endpoint). In addition, higher cut-off levels associated with neutralizing capacity and protective immunity were applied (i.e., > 15, > 100, > 141, and > 264 BAU/ml). A total of 169 patients were available for the 3-month follow-up. Overall, seroconversion at 3 months was similar between both groups (45 vs. 50% for mRNA and the vector group, respectively; p = 0.539). However, when applying higher cut-off levels, a significantly larger number of individuals in the vector group reached antibody levels > 141 and > 264 BAU/ml at the 3-month follow-up (141 BAU/ml: 4 vs. 15%, p = 0.009 and 264 BAU/ml: 1 vs. 10%, p = 0.018 for mRNA vs. the vector vaccine group, respectively). In line, antibody levels in seroconverted patients further increased from month 1 to month 3 in the vector group while remaining unchanged in the mRNA group (median increase: mRNA = 1.35 U/ml and vector = 27.6 U/ml, p = 0.004). Despite a similar overall seroconversion rate at 3 months following 3rd vaccination in KTR, a heterologous 3rd booster vaccination with Ad26COVS1 resulted in significantly higher antibody levels in responders.
Establishment and Cross-Protection Efficacy of a Recombinant Avian Gammacoronavirus Infectious Bronchitis Virus Harboring a Chimeric S1 Subunit
Authors: Ting Xiong , Xiang Chengwei , Liu Ding Xiang , Chen Ruiai
Published: July 2022

Infectious bronchitis virus (IBV) is a gammacoronavirus that causes a highly contagious disease in chickens and seriously endangers the poultry industry. A diversity of serotypes and genotypes of IBV have been identified worldwide, and the currently available vaccines do not cross-protect. In the present study, an efficient reverse genetics technology based on Beaudette-p65 has been used to construct a recombinant IBV, rIBV-Beaudette-KC(S1), by replacing the nucleotides 21,704–22,411 with the corresponding sequence from an isolate of QX-like genotype KC strain. Continuous passage of this recombinant virus in chicken embryos resulted in the accumulation of two point mutations (G21556C and C22077T) in the S1 region. Further studies showed that the T248S (G21556C) substitution may be essential for the adaptation of the recombinant virus to cell culture. Immunization of chicks with the recombinant IBV elicited strong antibody responses and showed high cross-protection against challenges with virulent M41 and a QX-like genotype IBV. This study reveals the potential of developing rIBV-Beau-KC(S1) as a cell-based vaccine with a broad protective immunity against two different genotypes of IBV.
Isolation, genomic characterization, and mushroom growth-promoting effect of the first fungus-derived Rhizobium
Authors: Hua Zhongyi , Liu Tianrui , Han Pengjie , Zhou Junhui , Zhao Yuyang , Huang Luqi , Yuan Yuan
Published: July 2022

Polyporus umbellatus is a well-known edible and medicinal mushroom, and some bacteria isolated from mushroom sclerotia may have beneficial effects on their host. These mushroom growth-promoting bacteria (MGPBs) are of great significance in the mushroom production. In this work, we aimed to isolate and identify MGPBs from P. umbellatus sclerotia. Using the agar plate dilution method, strain CACMS001 was isolated from P. umbellatus sclerotia. The genome of CACMS001 was sequenced using PacBio platform, and the phylogenomic analysis indicated that CACMS001 could not be assigned to known Rhizobium species. In co-culture experiments, CACMS001 increased the mycelial growth of P. umbellatus and Armillaria gallica and increased xylanase activity in A. gallica. Comparative genomic analysis showed that CACMS001 lost almost all nitrogen fixation genes but specially acquired one redox cofactor cluster with pqqE, pqqD, pqqC, and pqqB involved in the synthesis of pyrroloquinoline quinone, a peptide-derived redox participating in phosphate solubilization activity. Strain CACMS001 has the capacity to solubilize phosphate using Pikovskaya medium, and phnA and phoU involved in this process in CACMS001 were revealed by quantitative real-time PCR. CACMS001 is a new potential Rhizobium species and is the first identified MGPB belonging to Rhizobium. This novel bacterium would play a vital part in P. umbellatus, A. gallica, and other mushroom cultivation.
Comparison of fungal communities and nonvolatile flavor components in black Huangjiu formed using different inoculation fermentation methods
Authors: Li Pingping , Su Rui , Wang Qi , Liu Kunyi , Yang Hai , Du Wei , Li Zhengang , Chen Song , Xu Bin , Yang Wen
Published: July 2022

Black Huangjiu (BH) is a traditional alcoholic beverage in China, which is very popular among people. The different methods (simultaneous inoculation, sequential inoculation), were applied to ferment BH in this study, which were investigated the changes in the composition of fungal communities and non-volatile flavor compounds (nVFCs) by high-throughput sequencing (HTS) and ultraperformance liquid chromatography–tandem mass spectrometer (UPLC MS/MS). The results showed that Rhizopus and Saccharomyces were the predominant fungal genera throughout fermentation, and 471 nVFCs were detected in BH after fermentation. Compared to that observed simultaneous inoculation, Rhizopus increased at the end of sequential fermentation, and the contents of the organic acids and their derivatives increased significantly [variable importance in the projection (VIP) > 1.0, p < 0.05, fold change (FC) > 2], while that of lipids and lipid-like molecules decreased significantly (VIP > 1.0, p < 0.05, FC < 0.5). Through the correlation analysis of 32 nVFCs with significant differences (VIP > 1.0, p < 0.05, FC >32 or < 0.03) and the community, it was found that lipids and lipid-like molecules (12) and organic acids and their derivatives (10) were significantly (p < 0.05) negatively correlated with Saccharomyces, but they were significantly (p < 0.05) positively correlated with Rhizopus. Compared with simultaneous inoculation, BH fermented by sequential inoculation, the taste was stronger, sweeter, mellow, and softer. Our findings provide information on nVFC dynamics and will aid in the selection of beneficial strains to improve BH quality.
Modeling Energy Consumption Using Machine Learning
Authors: Sarswatula Sai Aravind , Pugh Tanna , Prabhu Vittaldas
Published: July 2022

Electrical, metal, plastic, and food manufacturing are among the major energy-consuming industries in the U.S. Since 1981, the U.S. Department of Energy Industrial Assessments Centers (IACs) have conducted audits to track and analyze energy data across several industries and provided recommendations for improving energy efficiency. In this article, we used statistical and machine learning techniques to draw insights from this IAC dataset with over 15,000 samples collected from 1981 to 2013. We developed predictive models for energy consumption using machine learning techniques such as Multiple Linear Regression, Random Forest Regressor, Decision Tree Regressor, and Extreme Gradient Boost Regressor. We also developed classifier models using Support Vector Machines, Random Forest, K-Nearest Neighbor (KNN), and deep learning. Results using this data set indicate that Random Forest Regressor is the best prediction technique with an R2 of 0.869, and the Random Forest classifier is the best technique with precision, recall, F1 score, and accuracy of 0.818, 0.884, 0.844, and 0.883, respectively. Deep learning also performed competitively with an accuracy of about 0.88 in training and testing after 10 epochs. The machine learning models could be useful in benchmarking the energy consumption of factories and identifying opportunities to improve energy efficiency.
Sex dimorphism in isoproterenol-induced cardiac damage associated neuroinflammation and behavior in old rats
Authors: Tóth Kata , Oroszi Tamás , van der Zee Eddy A. , Nyakas Csaba , Schoemaker Regien G.
Published: July 2022

Acute cardiac damage can be induced by isoproterenol injections in animals. The associated inflammatory response could be reflected in the brain as neuroinflammation, with potential consequences for brain function and behavior. Although cardiac responses are reported age and sex-related, for neuroinflammation and brain function this is virtually unknown. Therefore, cardiac damage and its consequences for neuroinflammation, brain function and behavior were compared in aged male and female rats. Wistar rats of 24 months of age were treated with isoproterenol (ISO, twice s.c.) or saline. Four weeks after injections, exploratory behavior and short-term memory were tested. Then, rats were sacrificed. Hearts were collected to measure cardiac damage. Brain tissue was collected to obtain measures of neuroinflammation and brain function. In male-, but not in female rats, ISO induced significant cardiac damage. Accordingly, mortality was higher in males than in females. Baseline hippocampal microglia activity was lower in females, while ISO induced neuroinflammation in both sexes, Hippocampal brain-derived neurotrophic factor expression appeared lower in females, without effects of ISO. In the open field test, ISO-treated males, but not females, displayed anxiety-like behavior. No effects of ISO were observed on short-term memory in either sex. In conclusion, sex dimorphism in effects of ISO was observed for cardiac damage and open field behavior. However, these effects could not be related to differences in hippocampal neuroinflammation or neuronal function.
Alzheimer-Compound Identification Based on Data Fusion and forgeNet_SVM
Authors: Yang Bin , Bao Wenzheng , Hong Shichai
Published: July 2022

Rapid screening and identification of potential candidate compounds are very important to understand the mechanism of drugs for the treatment of Alzheimer's disease (AD) and greatly promote the development of new drugs. In order to greatly improve the success rate of screening and reduce the cost and workload of research and development, this study proposes a novel Alzheimer-related compound identification algorithm namely forgeNet_SVM. First, Alzheimer related and unrelated compounds are collected using the data mining method from the literature databases. Three molecular descriptors (ECFP6, MACCS, and RDKit) are utilized to obtain the feature sets of compounds, which are fused into the all_feature set. The all_feature set is input to forgeNet_SVM, in which forgeNet is utilized to provide the importance of each feature and select the important features for feature extraction. The selected features are input to support vector machines (SVM) algorithm to identify the new compounds in Traditional Chinese Medicine (TCM) prescription. The experiment results show that the selected feature set performs better than the all_feature set and three single feature sets (ECFP6, MACCS, and RDKit). The performances of TPR, FPR, Precision, Specificity, F1, and AUC reveal that forgeNet_SVM could identify more accurately Alzheimer-related compounds than other classical classifiers.
Differential vulnerability of locus coeruleus and dorsal raphe neurons to chronic methamphetamine-induced degeneration
Authors: Du Yijuan , Choi Sanghoon , Pilski Alexander , Graves Steven M.
Published: July 2022

Methamphetamine (meth) increases monoamine oxidase (MAO)-dependent mitochondrial stress in axons of substantia nigra pars compacta (SNc), and ventral tegmental area (VTA) dopamine neurons. Chronic administration of meth results in SNc degeneration and MAO inhibition is neuroprotective, whereas, the VTA is resistant to degeneration. This differential vulnerability is attributed, at least in part, to the presence of L-type Ca2+ channel-dependent mitochondrial stress in SNc but not VTA dopamine neurons. MAO is also expressed in other monoaminergic neurons such as noradrenergic locus coeruleus (LC) and serotonergic dorsal raphe (DR) neurons. The impact of meth on mitochondrial stress in LC and DR neurons is unknown. In the current study we used a genetically encoded redox biosensor to investigate meth-induced MAO-dependent mitochondrial stress in LC and DR neurons. Similar to SNc and VTA neurons, meth increased MAO-dependent mitochondrial stress in axonal but not somatic compartments of LC norepinephrine and DR serotonin neurons. Chronic meth administration (5 mg/kg; 28-day) resulted in degeneration of LC neurons and MAO inhibition was neuroprotective whereas DR neurons were resistant to degeneration. Activating L-type Ca2+ channels increased mitochondrial stress in LC but not DR axons and inhibiting L-type Ca2+ channels in vivo with isradipine prevented meth-induced LC degeneration. These data suggest that similar to recent findings in SNc and VTA dopamine neurons, the differential vulnerability between LC and DR neurons can be attributed to the presence of L-type Ca2+ channel-dependent mitochondrial stress. Taken together, the present study demonstrates that both meth-induced MAO- and L-type Ca2+ channel-dependent mitochondrial stress are necessary for chronic meth-induced neurodegeneration.
Basketball training frequency is associated with executive functions in boys aged 6 to 8 years
Authors: Xu Yue , Zhang Wanxia , Zhang Kexin , Feng Min , Duan Tianqi , Chen Yilin , Wei Xuexiang , Luo Yanlin , Ni Guoxin
Published: July 2022

This study investigates the relationship between the frequency of basketball training and executive functions (inhibitory control, working memory, and cognitive flexibility) in boys aged 6 to 8. A total of 40 boys recruited from a local after-school basketball training club were divided into a low-frequency group (once a week) and a high-frequency group (at least twice a week). An additional 20 age-matched boys recruited from a local elementary school were considered as the control group (no training experience). All subjects conducted the Stop-signal task, the N-back task, and the switching task at rest. The mean reaction time and accuracy data obtained from each task were used in statistical analysis. There was no significant group difference in either the accuracy or reaction time of inhibitory control. Meanwhile, no significant difference was found in the reaction time of working memory across groups. However, the high-frequency group exhibited significantly higher accuracy (93.00 ± 4.31%) with regard to working memory than the low-frequency group (85.4 ± 6.04%, P < 0.001) and the control group (83.73 ± 7.70%, P < 0.001), respectively. A positive correlation was also found between the accuracy of working memory and groups. Furthermore, in comparison with the control group, the high-frequency group exhibited significantly higher cognitive flexibility accuracy (91.93 ± 7.40% vs. 85.70 ± 9.75%, P = 0.004) and shorter reaction time (934.24 ± 213.02 ms vs. 1,122.06 ± 299.14 ms, P < 0.001). There was also a positive correlation between the accuracy of cognitive flexibility and groups. These findings suggest that regular basketball training, especially with higher frequency, is beneficial to working memory and cognitive flexibilityin boys aged 6 to 8.
Patterned Hippocampal Stimulation Facilitates Memory in Patients With a History of Head Impact and/or Brain Injury
Authors: Roeder Brent M. , Riley Mitchell R. , She Xiwei , Dakos Alexander S. , Robinson Brian S. , Moore Bryan J. , Couture Daniel E. , Laxton Adrian W. , Popli Gautam , Munger Clary Heidi M. , Sam Maria , Heck Christi , Nune George , Lee Brian , Liu Charles , Shaw Susan , Gong Hui , Marmarelis Vasilis Z. , Berger Theodore W. , Deadwyler Sam A. , Song Dong , Hampson Robert E.
Published: July 2022

Rationale: Deep brain stimulation (DBS) of the hippocampus is proposed for enhancement of memory impaired by injury or disease. Many pre-clinical DBS paradigms can be addressed in epilepsy patients undergoing intracranial monitoring for seizure localization, since they already have electrodes implanted in brain areas of interest. Even though epilepsy is usually not a memory disorder targeted by DBS, the studies can nevertheless model other memory-impacting disorders, such as Traumatic Brain Injury (TBI). Methods: Human patients undergoing Phase II invasive monitoring for intractable epilepsy were implanted with depth electrodes capable of recording neurophysiological signals. Subjects performed a delayed-match-to-sample (DMS) memory task while hippocampal ensembles from CA1 and CA3 cell layers were recorded to estimate a multi-input, multi-output (MIMO) model of CA3-to-CA1 neural encoding and a memory decoding model (MDM) to decode memory information from CA3 and CA1 neuronal signals. After model estimation, subjects again performed the DMS task while either MIMO-based or MDM-based patterned stimulation was delivered to CA1 electrode sites during the encoding phase of the DMS trials. Each subject was sorted (post hoc) by prior experience of repeated and/or mild-to-moderate brain injury (RMBI), TBI, or no history (control) and scored for percentage successful delayed recognition (DR) recall on stimulated vs. non-stimulated DMS trials. The subject’s medical history was unknown to the experimenters until after individual subject memory retention results were scored. Results: When examined compared to control subjects, both TBI and RMBI subjects showed increased memory retention in response to both MIMO and MDM-based hippocampal stimulation. Furthermore, effects of stimulation were also greater in subjects who were evaluated as having pre-existing mild-to-moderate memory impairment. Conclusion: These results show that hippocampal stimulation for memory facilitation was more beneficial for subjects who had previously suffered a brain injury (other than epilepsy), compared to control (epilepsy) subjects who had not suffered a brain injury. This study demonstrates that the epilepsy/intracranial recording model can be extended to test the ability of DBS to restore memory function in subjects who previously suffered a brain injury other than epilepsy, and support further investigation into the beneficial effect of DBS in TBI patients.
Synergistic photobiomodulation with 808-nm and 1064-nm lasers to reduce the β-amyloid neurotoxicity in the in vitro Alzheimer's disease models
Authors: Zhang Renlong , Zhou Ting , Samanta Soham , Luo Ziyi , Li Shaowei , Xu Hao , Qu Junle
Published: July 2022

Background

In Alzheimer's disease (AD), the deposition of β-amyloid (Aβ) plaques is closely associated with the neuronal apoptosis and activation of microglia, which may result in the functional impairment of neurons through pro-inflammation and over-pruning of the neurons. Photobiomodulation (PBM) is a non-invasive therapeutic approach without any conspicuous side effect, which has shown promising attributes in the treatment of chronic brain diseases such as AD by reducing the Aβ burden. However, neither the optimal parameters for PBM treatment nor its exact role in modulating the microglial functions/activities has been conclusively established yet.

Methods

An inflammatory stimulation model of Alzheimer's disease (AD) was set up by activating microglia and neuroblastoma with fibrosis β-amyloid (fAβ) in a transwell insert system. SH-SY5Y neuroblastoma cells and BV2 microglial cells were irradiated with the 808- and 1,064-nm lasers, respectively (a power density of 50 mW/cm2 and a dose of 10 J/cm2) to study the PBM activity. The amount of labeled fAβ phagocytosed by microglia was considered to assess the microglial phagocytosis. A PBM-induced neuroprotective study was conducted with the AD model under different laser parameters to realize the optimal condition. Microglial phenotype, microglial secretions of the pro-inflammatory and anti-inflammatory factors, and the intracellular Ca2+ levels in microglia were studied in detail to understand the structural and functional changes occurring in the microglial cells of AD model upon PBM treatment.

Conclusion

A synergistic PBM effect (with the 808- and 1,064-nm lasers) effectively inhibited the fAβ-induced neurotoxicity of neuroblastoma by promoting the viability of neuroblastoma and regulating the intracellular Ca2+ levels of microglia. Moreover, the downregulation of Ca2+ led to microglial polarization with an M2 phenotype, which promotes the fAβ phagocytosis, and resulted in the upregulated expression of anti-inflammatory factors and downregulated expression of inflammatory factors.
Neuroanatomical predictors of complex skill acquisition during video game training
Authors: Kovbasiuk Anna , Lewandowska Paulina , Brzezicka Aneta , Kowalczyk-Grębska Natalia
Published: July 2022

It is known that the outcomes of complex video game (VG) skill acquisition are correlated with individual differences in demographic and behavioral variables, such as age, intelligence and visual attention. However, empirical studies of the relationship between neuroanatomical features and success in VG training have been few and far between. The present review summarizes existing literature on gray matter (GM) and white matter correlates of complex VG skill acquisition as well as explores its relationship with neuroplasticity. In particular, since age can be an important factor in the acquisition of new cognitive skills, we present studies that compare different age groups (young and old adults). Our review reveals that GM in subcortical brain areas predicts complex VG learning outcomes in young subjects, whereas in older subjects the same is true of cortical frontal areas. This may be linked to age-related compensatory mechanisms in the frontal areas, as proposed by The Scaffolding Theory of Aging and Cognition. In the case of plasticity, there is no such relationship – in the group of younger and older adults there are changes after training in both cortical and subcortical areas. We also summarize best practices in research on predictors of VG training performance and outline promising areas of research in the study of complex video game skill acquisition.