bluuebunny/crossref_metadata_2025_split huggingface dataset:
Harmful algae diversity from a coastal upwelling system detected by high-throughput sequencing
Authors: Ríos-Castro Raquel , Novoa Beatriz , Hernández-Urcera Jorge , Rodríguez Francisco , Figueras Antonio 
Published: June 2023

IntroductionIn recent years, environmental DNA (eDNA) amplicon sequencing has been used to unveil plankton diversity in the field. Nevertheless, molecular methods, such as this, are rarely used in harmful algal bloom (HAB) monitoring programs, which mainly rely on morphological identification by conventional light microscopy.MethodsThe present study focused on a shallow marine environment (Ría de Vigo, Northwest Spain), where sediment and plankton samples were collected from 2016 to 2018.ResultsThe application of eDNA amplicon sequencing allowed us to simultaneously detect 25 potential harmful species (mainly diatoms and dinoflagellates) included in the IOC-UNESCO Taxonomic Reference List of Harmful Microalgae. Among these, causative agents of amnesic shellfish poisoning (Pseudo-nitzschia spp.) paralytic shellfish poisoning (Gymnodinium catenatum and Alexandrium minutum), azaspiracid producers (Azadinium poporum) and ichthyotoxic haptophytes (Chrysochromulina leadbeateri), were identified. Some toxic microalgae were better represented in sediment (e.g., Pseudo-nitzschia pungens, Gymnodinium catenatum) or planktonic fractions (e.g., Pseudo-nitzschia, Gymnodinium smaydae), confirming the importance of including both sediment and plankton fractions in eDNA monitoring studies. Despite the limitations of sequencing short amplicons, it was possible to discern in this study six Pseudo-nitzschia species and associate each of them with each seasonal peak produced in summer periods. Furthermore, several species previously unreported in Ría de Vigo (Pseudo-nitzschia turgidula, Chrysochromulina leadbeateri, Azadinium poporum) could be detected.DiscusionThese results point out the application of eDNA amplicon sequencing to expand our knowledge about harmful species in HAB monitoring programs and early warning systems for low abundant and rare taxa.
Isoacids supplementation improves growth performance and feed fiber digestibility associated with ruminal bacterial community in yaks
Authors: Jiang Fei , Gao Yanhua , Peng Zhongli , Ma Xiulian , You Yinjie , Hu Zhibin , He Anxiang , Liao Yupeng 
Published: June 2023

IntroductionThis study was conducted to assess the effect of mixed isoacid (MI) supplementation on fermentation characteristics, nutrient apparent digestibility, growth performance, and rumen bacterial community in yaks.MethodsA 72-h in vitro fermentation experiment was performed on an ANKOM RF gas production system. MI was added to five treatments at doses of 0, 0.1%, 0.2%, 0.3%, 0.4%, and 0.5% on the dry matter (DM) basis of substrates using a total of 26 bottles (4 bottles per treatment and 2 bottles as the blank). Cumulative gas production was measured at 4, 8, 16, 24, 36, 48, and 72 h. Fermentation characteristics including pH, the concentration of volatile fatty acids (VFAs), ammonia nitrogen (NH3-N), microbial proteins (MCP), and the disappearance rate of dry matter (DMD), neutral detergent fiber (NDFD), and acid detergent fiber (ADFD) were measured after a 72-h in vitro fermentation to determine an optimal MI dose. Fourteen Maiwa male yaks (180–220 kg, 3–4 years old of age) were randomly assigned to the control group (without MI, n = 7) and the supplemented MI group (n = 7, supplemented with 0.3% MI on DM basis) for the 85-d animal experiment. Growth performance, nutrient apparent digestibility, rumen fermentation parameters, and rumen bacterial diversity were measured.ResultsSupplementation with 0.3% MI achieved the greatest propionate and butyrate content, NDFD and ADFD compared with other groups (P &lt; 0.05). Therefore, 0.3% was used for the animal experiment. Supplementation with 0.3% MI significantly increased the apparent digestibility of NDF and ADF (P &lt; 0.05), and the average daily weight gain of yaks (P &lt; 0.05) without affecting the ruminal concentration of NH3-N, MCP, and VFAs. 0.3% MI induced rumen bacteria to form significantly different communities when compared to the control group (P &lt; 0.05). g__norank_f__Bacteroidales_BS11_gut_group, g__norank_f__Muribaculaceae, g__Veillonellaceae_UCG-001, g__Ruminococcus_gauvreauii_group, g__norank_f__norank_o__RF39 and g__Flexilinea were identified as the biomarker taxa in responding to supplementation with 0.3% MI. Meanwhile, the abundance of g__Flexilinea and g__norank_f__norank_o__RF39 were significantly positively correlated with the NDF digestibility (P &lt; 0.05).ConclusionIn conclusion, supplementation with 0.3% MI improved the in vitro rumen fermentation characteristics, feed fiber digestibility, and growth performance in yaks, which was associated with changes of the abundance of g__Flexilinea and g__norank_f__norank_o__RF39.
Bacteriophage-mediated biosynthesis of MnO2NPs and MgONPs and their role in the protection of plants from bacterial pathogens
Authors: Ogunyemi Solabomi Olaitan , Abdallah Yasmine , Ibrahim Ezzeldin , Zhang Yang , Bi Ji’an , Wang Fang , Ahmed Temoor , Alkhalifah Dalal Hussien M. , Hozzein Wael N. , Yan Chengqi , Li Bin , Xu Lihui 
Published: June 2023

IntroductionXanthomonas oryzae pv. oryzae (Xoo) is the plant pathogen of Bacterial Leaf Blight (BLB), which causes yield loss in rice.MethodsIn this study, the lysate of Xoo bacteriophage X3 was used to mediate the bio-synthesis of MgO and MnO2. The physiochemical features of MgONPs and MnO2NPs were observed via Ultraviolet - Visible spectroscopy (UV–Vis), X-ray diffraction (XRD), Transmission/Scanning electron microscopy (TEM/SEM), Energy dispersive spectrum (EDS), and Fourier-transform infrared spectrum (FTIR). The impact of nanoparticles on plant growth and bacterial leaf blight disease were evaluated. Chlorophyll fluorescence was used to determine whether the nanoparticles application were toxic to the plants.ResultsAn absorption peak of 215 and 230 nm for MgO and MnO2, respectively, confirmed nanoparticle formation via UV–Vis. The crystalline nature of the nanoparticles was detected by the analysis of XRD. Bacteriological tests indicated that MgONPs and MnO2NPs sized 12.5 and 9.8 nm, respectively, had strong in vitro antibacterial effects on rice bacterial blight pathogen, Xoo. MnO2NPs were found to have the most significant antagonist effect on nutrient agar plates, while MgONPs had the most significant impact on bacterial growth in nutrient broth and on cellular efflux. Furthermore, no toxicity to plants was observed for MgONPs and MnO2NPs, indeed, MgONPs at 200 μg/mL significantly increased the quantum efficiency of PSII photochemistry on the model plant, Arabidopsis, in light (ΦPSII) compared to other interactions. Additionally, significant suppression of BLB was noted in rice seedlings amended with the synthesized MgONPs and MnO2NPs. MnO2NPs showed promotion of plant growth in the presence of Xoo compared to MgONPs.ConclusionAn effective alternative for the biological production of MgONPs and MnO2NPs was reported, which serves as an effective substitute to control plant bacterial disease with no phytotoxic effect.
Identifying potential drug-target interactions based on ensemble deep learning
Authors: Zhou Liqian , Wang Yuzhuang , Peng Lihong , Li Zejun , Luo Xueming 
Published: June 2023

IntroductionDrug-target interaction prediction is one important step in drug research and development. Experimental methods are time consuming and laborious.MethodsIn this study, we developed a novel DTI prediction method called EnGDD by combining initial feature acquisition, dimensional reduction, and DTI classification based on Gradient boosting neural network, Deep neural network, and Deep Forest.ResultsEnGDD was compared with seven stat-of-the-art DTI prediction methods (BLM-NII, NRLMF, WNNGIP, NEDTP, DTi2Vec, RoFDT, and MolTrans) on the nuclear receptor, GPCR, ion channel, and enzyme datasets under cross validations on drugs, targets, and drug-target pairs, respectively. EnGDD computed the best recall, accuracy, F1-score, AUC, and AUPR under the majority of conditions, demonstrating its powerful DTI identification performance. EnGDD predicted that D00182 and hsa2099, D07871 and hsa1813, DB00599 and hsa2562, D00002 and hsa10935 have a higher interaction probabilities among unknown drug-target pairs and may be potential DTIs on the four datasets, respectively. In particular, D00002 (Nadide) was identified to interact with hsa10935 (Mitochondrial peroxiredoxin3) whose up-regulation might be used to treat neurodegenerative diseases. Finally, EnGDD was used to find possible drug targets for Parkinson's disease and Alzheimer's disease after confirming its DTI identification performance. The results show that D01277, D04641, and D08969 may be applied to the treatment of Parkinson's disease through targeting hsa1813 (dopamine receptor D2) and D02173, D02558, and D03822 may be the clues of treatment for patients with Alzheimer's disease through targeting hsa5743 (prostaglandinendoperoxide synthase 2). The above prediction results need further biomedical validation.DiscussionWe anticipate that our proposed EnGDD model can help discover potential therapeutic clues for various diseases including neurodegenerative diseases.
Efficacy of acupuncture and pharmacological therapies for vascular cognitive impairment with no dementia: a network meta-analysis
Authors: Li Ruiyu , Xu Congcong , Zhong Pengyu , Wang Ke , Luo YinXiang , Xiao Lingyong , Dai Xiaoyu , Han Jingxian , Zhang Xuezhu 
Published: June 2023

Background and objectiveVascular cognitive impairment with no dementia (VCIND) is considered to be the prodromal stage of vascular dementia, characterized by insidious onset. Although acupuncture and drug therapies are effective, the optimal therapy for VCIND remains to be further determined. Therefore, we conducted a network meta-analysis to compare the effectiveness of acupuncture therapies and current common medicines for VCIND.MethodsWe searched eight electronic databases to identify eligible randomized controlled trials of patients with VCIND treated by acupuncture or drug therapies. The primary outcome was Montreal Cognitive Assessment, and the secondary outcome was Mini-Mental State Examination. We conducted the network meta-analysis within a Bayesian framework. Weighted mean difference with 95% confidence intervals were applied as effect sizes to continuous data for all outcomes. Sensitivity analysis was done to assess the robustness of the findings, and we also carried out a subgroup analysis based on age. We assessed the risk of bias using the Risk of Bias 2.0 tool and applied the Grade of Recommendation Assessment, Development and Evaluation (GRADE) to assess the quality of the outcomes. This study was registered with PROSPERO, number CRD42022331718.ResultsA total of 33 studies with 14 interventions were included, including 2603 participants. In terms of the primary outcome, manual acupuncture plus herbal decoction was considered to be the most effective intervention (P = 91.41%), followed by electroacupuncture (P = 60.77%) and manual acupuncture plus piracetam (P = 42.58%), whereas donepezil hydrochloride ranked the least efficacious intervention (P = 54.19%). For the secondary outcome, electroacupuncture plus nimodipine was considered to be the most effective intervention (P = 42.70%), followed by manual acupuncture plus nimodipine (P = 30.62%) and manual acupuncture (P = 28.89%), whereas nimodipine ranked the least efficacious intervention (P = 44.56%).ConclusionManual acupuncture plus herbal decoction might be the most effective intervention for VCIND. The combination of acupuncture and drug therapy had a tendency to perform better than monotherapy in terms of clinical outcomes.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=331718, identifier: CRD42022331718.
Dorsal striatum c-Fos activity in perseverative ephrin-A2A5−/− mice and the cellular effect of low-intensity rTMS
Authors: Tomar Maitri , Rodger Jennifer , Moretti Jessica 
Published: June 2023

IntroductionOverreliance on habit is linked with disorders, such as drug addiction and obsessive-compulsive disorder, and there is increasing interest in the use of repetitive transcranial magnetic stimulation (rTMS) to alter neuronal activity in the relevant pathways and for therapeutic outcomes. In this study, we researched the brains of ephrin-A2A5−/− mice, which previously showed perseverative behavior in progressive-ratio tasks, associated with low cellular activity in the nucleus accumbens. We investigated whether rTMS treatment had altered the activity of the dorsal striatum in a way that suggested altered hierarchical recruitment of brain regions from the ventral striatum to the dorsal striatum, which is linked to abnormal habit formation.MethodsBrain sections from a limited number of mice that underwent training and performance on a progressive ratio task with and without low-intensity rTMS (LI-rTMS) were taken from a previous study. We took advantage of the previous characterization of perseverative behavior to investigate the contribution of different neuronal subtypes and striatal regions within this limited sample. Striatal regions were stained for c-Fos as a correlate of neuronal activation for DARPP32 to identify medium spiny neurons (MSNs) and for GAD67 to identify GABA-ergic interneurons.Results and discussionContrary to our hypothesis, we found that neuronal activity in ephrin-A2A5−/− mice still reflected the typical organization of goal-directed behavior. There was a significant difference in the proportion of neuronal activity across the striatum between experimental groups and control but no significant effects identifying a specific regional change. However, there was a significant group by treatment interaction which suggests that MSN activity is altered in the dorsomedial striatum and a trend suggesting that rTMS increases ephrin-A2A5−/− MSN activity in the DMS. Although preliminary and inconclusive, the analysis of this archival data suggests that investigating circuit-based changes in striatal regions may provide insight into chronic rTMS mechanisms that could be relevant to treating disorders associated with perseverative behavior.
Clinical study of melodic intonation therapy combined with transcranial direct current stimulation for post-stroke aphasia: a single-blind, randomized controlled trial
Authors: Yan Zhijie , He Xinyuan , Cheng Mangmang , Fan Xiaoqing , Wei Dongshuai , Xu Shuo , Li Chong , Li Xiaofang , Xing Hongxia , Jia Jie 
Published: June 2023

BackgroundGlobally, more than 10 million new stroke cases occur annually, of which aphasia accounts for about one-third. Aphasia has become an independent predictor of functional dependence and death for the stroke population. The closed-loop rehabilitation of combining behavioral therapy with central nerve stimulation seems to be the research trend of post-stroke aphasia (PSA) due to its advantages in improving linguistic deficits.ObjectiveTo verify the clinical efficacy of a closed-loop rehabilitation program combining melodic intonation therapy (MIT) with transcranial direct current stimulation (tDCS) for PSA.MethodsThis was a single-center, assessor-blinded, randomized controlled clinical trial, which screened 179 patients and included 39 PSA subjects, with the registration number ChiCTR2200056393 in China. Demographic and clinical data were documented. The primary outcome was the Western Aphasia Battery (WAB) used to assess language function, and the secondary outcomes included Montreal Cognitive Assessment (MoCA), Fugl-Meyer Assessment (FMA), and Barthel Index (BI) for evaluating cognition, motor, and activities of daily living, respectively. With the computer-generated randomization sequence, subjects were randomly divided into the conventional group (CG), MIT combined with sham stimulation group (SG), and MIT combined with tDCS group (TG). After the three-week intervention, the functional changes in each group were analyzed by the paired sample T-test, and the functional difference between the three groups was analyzed by ANOVA.ResultsThere was no statistical difference on the baseline. After the intervention, the WAB’s aphasia quotient (WAB-AQ), MoCA, FMA, and BI were statistically different in SG and TG, including all the sub-items in WAB and FMA, while only listening comprehension, FMA, and BI were statistically different in CG. The differences of WAB-AQ, MoCA, and FMA were statistically different among the three groups, but BI was not. The post hoc test results revealed that the changes of WAB-AQ and MoCA in TG were more significant than the others.ConclusionMIT combined with tDCS can augment the positive effect on language and cognitive recovery in PSA.
Anodal transcranial direct current stimulation (tDCS) over the left dorsolateral prefrontal cortex improves attentional control in chronically stressed adults
Authors: Liu Yong , Liu Qingjin , Zhao Jia , Leng Xuechen , Han Jinfeng , Xia Feng , Pang Yazhi , Chen Hong 
Published: June 2023

IntroductionChronic stress is a long-term condition that negatively affects cognitive ability and mental health. Individuals who experience chronic stress show poor attentional control. Transcranial direct current stimulation (tDCS) to the dorsolateral prefrontal cortex (DLPFC) modulates executive function domains. Therefore, it is beneficial to investigate whether tDCS of the DLPFC could improve attentional control and relieve stress in chronically stressed individuals.MethodsWe assess the event-related potentials (ERPs) associated with attentional control in individuals with chronic stress after the tDCS intervention. Forty individuals were randomly assigned to either the anodal tDCS group, which received 5 sessions of the 20 min tDCS over the DLPFC (2 mA; n = 20), or the sham tDCS (n = 20). Participants’ stress levels, anxiety, depressive symptoms, and state affects were assessed and compared before and after the intervention. The ERP was collected through electroencephalography (EEG) technology during an attentional network test.ResultsAfter the anodal tDCS, we found a significant decrease in the perceived stress scale (PSS) scores (from an average score of 35.05 to 27.75), p = 0.01 as well as the State-Trait Anxiety Inventory (STAI) scores, p = 0.002. Better performance in the attentional network test, a significant reduction in the N2 amplitudes, and an enhancement in the P3 amplitudes (both cues and targets) were also found in the anodal tDCS group.DiscussionOur study findings suggest that tDCS to the left DLPFC could effectively relieve chronic stress, potentially reflected by increased attentional control.
Relationship between placental pathology and neonatal outcomes
Authors: Guo Xiaojun , Wang Yixiao , Yu Hong 
Published: June 2023

ObjectiveTo evaluate the relationship between maternal vascular malperfusion and acute intrauterine infection/inflammation with neonatal outcomes.MethodsThis was a retrospective study of women with singleton pregnancies who completed placenta pathological examination. The aim was to study the distribution of acute intrauterine infection/inflammation and maternal placental vascular malperfusion among groups with preterm birth and/or rupture of membranes. The relationship between two subtypes of placental pathology and neonatal gestational age, birth weight Z-score, neonatal respiratory distress syndrome, and intraventricular hemorrhage was further explored.Results990 pregnant women were divided into four groups, including 651 term, 339 preterm, 113 women with premature rupture of membranes, and 79 with preterm premature rupture of membranes. The incidence of respiratory distress syndrome and intraventricular hemorrhage in four groups were (0.7%, 0.0%, 31.9%, 31.6%, P &lt; 0.001) and (0.9%, 0.9%, 20.0%, 17.7%, P &lt; 0.001), respectively. The incidence of maternal vascular malperfusion and acute intrauterine infection/inflammation were (82.0%, 77.0%, 75.8%, 72.1%, P = 0.06) and (21.9%, 26.5%, 23.1%, 44.3%, P = 0.010), respectively. Acute intrauterine infection/inflammation was associated with shorter gestational age (adjusted difference −4.7 weeks, P &lt; 0.001) and decreased weight (adjusted Z score −2.6, P &lt; 0.001) than those with no lesions in preterm birth. When two subtype placenta lesions co-occurrence, shorter gestational age (adjusted difference −3.0 weeks, P &lt; 0.001) and decreased weight (adjusted Z score −1.8, P &lt; 0.001) were observed in preterm. Consistent findings were observed in preterm births with or without premature rupture of membranes. In addition, acute infection/inflammation and maternal placenta malperfusion alone or in combination were associated with an increased risk of neonatal respiratory distress syndrome (adjusted odds ratio (aOR) 0.8, 1.5, 1.8), but the difference was not statistically significant.ConclusionMaternal vascular malperfusion and acute intrauterine infection/inflammation alone or co-occurrence are associated with adverse neonatal outcomes, which may provide new ideas for clinical diagnosis and treatment.
Metabolism and toxicity of usnic acid and barbatic acid based on microsomes, S9 fraction, and 3T3 fibroblasts in vitro combined with a UPLC-Q-TOF-MS method
Authors: Wang Hanxue , Xuan Min , Diao Juanjuan , Xu Nan , Li Manlin , Huang Cheng , Wang Changhong 
Published: June 2023

Introduction: Usnic acid (UA) and barbatic acid (BA), two typical dibenzofurans and depsides in lichen, have a wide range of pharmacological activities and hepatotoxicity concerns. This study aimed to clarify the metabolic pathway of UA and BA and illuminate the relationship between metabolism and toxicity.Methods: An UPLC-Q-TOF-MS method was developed for metabolite identification of UA and BA in human liver microsomes (HLMs), rat liver microsomes (RLMs), and S9 fraction (RS9). The key metabolic enzymes responsible for UA and BA were identified by enzyme inhibitors combined with recombinant human cytochrome P450 (CYP450) enzymes. The cytotoxicity and metabolic toxicity mechanism of UA and BA were determined by the combination model of human primary hepatocytes and mouse 3T3 fibroblasts.Results: The hydroxylation, methylation, and glucuronidation reactions were involved in the metabolic profiles of UA and BA in RLMs, HLMs, and RS9. CYP2C9, CYP3A4, CYP2C8, and UGT1A1 are key metabolic enzymes responsible for metabolites of UA and CYP2C8, CYP2C9, CYP2C19, CYP1A1, UGT1A1, UGT1A3, UGT1A7, UGT1A8, UGT1A9, and UGT1A10 for metabolites of BA. UA and BA did not display evident cytotoxicity in human primary hepatocytes at concentrations of 0.01–25 and 0.01–100 µM, respectively, but showed potential cytotoxicity to mouse 3T3 fibroblasts with 50% inhibitory concentration values of 7.40 and 60.2 µM.Discussion: In conclusion, the attenuated cytotoxicity of BA is associated with metabolism, and UGTs may be the key metabolic detoxification enzymes. The cytotoxicity of UA may be associated with chronic toxicity. The present results provide important insights into the understanding of the biotransformation behavior and metabolic detoxification of UA and BA.