bluuebunny/crossref_metadata_2025 huggingface dataset:
Visual search and the inhibitions of return
Authors: Klein Raymond M. , Redden Ralph S. , Hilchey Matthew D.
Published: May 2023

In the early 1980's independent research streams were launched by two of the 20th century's leading attention researchers. Anne Treisman's research program is best-known for distinguishing empirically between serial and pop-out search and for proposing feature integration theory and the idea of an attentional operator, that sequentially inspects items or groups of items when search is difficult. Among his many contributions to psychological science, Michael Posner is well-known for pioneering simple model tasks that made the allocation of visual attention in space amenable to scientific inquiry. When one version of the Posner cuing paradigm was used to explore visuospatial orienting it was serendipitously discovered that an “inhibitory” effect occurred in the aftermath of events that captured visuospatial attention involuntarily. This “inhibitory” phenomenon became known as Inhibition of Return (IOR), and, as implied by its name, the underlying mechanisms were thought to bias attention away from previously explored places. These two research programs were linked in 1988 when Raymond Klein exploited the distinction between pop-out and serial search to test and verify Posner's proposal that this inhibition might be a novelty seeking mechanism that could improve search efficiency. Subsequent research has identified at least two different inhibitory mechanisms that bias attention toward novelty. We present evidence using several diagnostics (central vs. peripheral targets, joint consideration of speed and accuracy, and the locus of slack logic embedded in the psychological refractory period effect) to illustrate the dual natures of IOR. The input form operates on a salience map that influences what will capture our attention, while the output form operates on a priority map that influences what behaviors (including orienting) are likely to be executed. The input form is generated when the reflexive oculomotor system is suppressed while the output form is generated when this system is not suppressed. We believe that both forms of IOR can serve the novelty seeking (and search facilitating) function proposed by Posner and others. Yet, many questions remain unanswered. Some of the many remaining puzzles will be described and we hope that our review will stimulate research to solve them.
Shape-selective processing in deep networks: integrating the evidence on perceptual integration
Authors: Jarvers Christian , Neumann Heiko
Published: May 2023

Understanding how deep neural networks resemble or differ from human vision becomes increasingly important with their widespread use in Computer Vision and as models in Neuroscience. A key aspect of human vision is shape: we decompose the visual world into distinct objects, use cues to infer their 3D geometries, and can group several object parts into a coherent whole. Do deep networks use the shape of objects similarly when they classify images? Research on this question has yielded conflicting results, with some studies showing evidence for shape selectivity in deep networks, while others demonstrated clear deficiencies. We argue that these conflicts arise from differences in experimental methods: whether studies use custom images in which only some features are available, images in which different features compete, image pairs that vary along different feature dimensions, or large sets of images to assess how representations vary overall. Each method offers a different, partial view of shape processing. After comparing their advantages and pitfalls, we propose two hypotheses that can reconcile previous results. Firstly, deep networks are sensitive to local, but not global shape. Secondly, the higher layers of deep networks discard some of the shape information that the lower layers are sensitive to. We test these hypotheses by comparing network representations for natural images and silhouettes in which local or global shape is degraded. The results support both hypotheses, but for different networks. Purely feed-forward convolutional networks are unable to integrate shape globally. In contrast, networks with residual or recurrent connections show a weak selectivity for global shape. This motivates further research into recurrent architectures for perceptual integration.
Catheter ablation in Asian patients with atrial fibrillation and hypertrophic cardiomyopathy: electrophysiological characteristics of recurrence and long-term clinical outcomes
Authors: Lin Chih-Hsien , Lin Chin-Yu , Chung Fa-Po , Lin Yenn-Jiang , Chang Shih-Lin , Lo Li-Wei , Hu Yu-Feng , Chao Tze-Fan , Liao Jo-Nan , Chang Ting-Yung , Tuan Ta-Chuan , Kuo Ling , Wu Cheng-I , Liu Chih-Min , Liu Shin-Huei , Li Guan-Yi , Kuo Ming-Jen , Weng Chi-Jen , Chen Shih-Ann
Published: May 2023

Background

Catheter ablation (CA) is a treatment strategy for atrial fibrillation (AF) in patients with hypertrophic cardiomyopathy (HCM). We investigated the electrophysiological characteristics of recurrence in a tertiary referral center and compared long-term clinical outcomes after CA therapy with patients who did not undergo CA.

Methods

Patients with HCM and AF who underwent CA (group 1, n = 60) or pharmacological treatment (group 2, n = 298) between 2006 and 2021 were enrolled in this study. The baseline characteristics and electrophysiological characteristics of group 1 patients were examined to elucidate the reason for the recurrence of AF after CA therapy. The clinical results of the patients in Group 1 and Group 2 were compared using a propensity score (PS)-matched method.

Results

The most common cause of recurrence was pulmonary vein reconnection (86.5%), followed by non-pulmonary vein triggers (40.5%), cavotricuspid isthmus flutter (29.7%), and atypical flutter (24.3%). Thyroid disease (HR, 14.713; P < 0.01), diabetes (HR, 3.074; P = 0.03), and non-paroxysmal AF (HR, 4.012; P = 0.01); these factors independently predicted recurrence. After the first recurrence, patients who underwent repeat CA showed a better arrhythmia-free state (74.1%) than those who underwent drug escalation therapy (29.4%, P < 0.01). After matching, PS-group 1 patients showed significantly better outcomes in all-cause mortality, heart failure hospitalization, and left atrial reverse remodeling than PS-group 2 patients.

Conclusions

Patients who underwent CA showed better clinical outcomes than those who underwent drug therapy. The main predictors of recurrence were thyroid disease, diabetes, and non-paroxysmal AF.
The let-7b-5p, miR-326, and miR-125a-3p are associated with left ventricular systolic dysfunction in post-myocardial infarction
Authors: Dantas-Komatsu Raquel Costa Silva , Cruz Marina Sampaio , Freire Paula Paccielli , Diniz Rosiane Viana Zuza , Bortolin Raul Hernandes , Cabral-Marques Otávio , Souza Kamilla Batista da Silva , Hirata Mario Hiroyuki , Hirata Rosario Dominguez Crespo , Reis Bruna Zavarize , Jurisica Igor , Silbiger Vivian Nogueira , Luchessi Andre Ducati
Published: May 2023

Background

Acute ST-elevation myocardial infarction (STEMI) can lead to adverse cardiac remodeling, resulting in left ventricular systolic dysfunction (LVSd) and heart failure. Epigenetic regulators, such as microRNAs, may be involved in the physiopathology of LVSd.

Objective

This study explored microRNAs in peripheral blood mononuclear cells (PBMC) of post-myocardial infarction patients with LVSd.

Methods

Post-STEMI patients were grouped as having (LVSd, n = 9) or not LVSd (non-LVSd, n = 16). The expression of 61 microRNAs was analyzed in PBMC by RT-qPCR and the differentially expressed microRNAs were identified. Principal Component Analysis stratified the microRNAs based on the development of dysfunction. Predictive variables of LVSd were investigated through logistic regression analysis. A system biology approach was used to explore the regulatory molecular network of the disease and an enrichment analysis was performed.

Results

The let-7b-5p (AUC: 0.807; 95% CI: 0.63–0.98; p = 0.013), miR-125a-3p (AUC: 0.800; 95% CI: 0.61–0.99; p = 0.036) and miR-326 (AUC: 0.783; 95% CI: 0.54–1.00; p = 0.028) were upregulated in LVSd (p < 0.05) and discriminated LVSd from non-LVSd. Multivariate logistic regression analysis showed let-7b-5p (OR: 16.00; 95% CI: 1.54–166.05; p = 0.020) and miR-326 (OR: 28.00; 95% CI: 2.42–323.70; p = 0.008) as predictors of LVSd. The enrichment analysis revealed association of the targets of these three microRNAs with immunological response, cell-cell adhesion, and cardiac changes.

Conclusion

LVSd alters the expression of let-7b-5p, miR-326, and miR-125a-3p in PBMC from post-STEMI, indicating their potential involvement in the cardiac dysfunction physiopathology and highlighting these miRNAs as possible LVSd biomarkers.
Using association rules analysis to determine favorable mineralization sites in the Jiaojia gold belt, Jiaodong Peninsula, East China
Authors: Mao Xiancheng , Tang Miao , Deng Hao , Chen Jin , Liu Zhankun , Wang Jinli
Published: May 2023

Mesozoic orogenic gold deposits in the Jiaojia goldfield, Eastern China show the features of regular mineralization spatial distribution and have long been captivated the attention of geologists. This study integrates 3D modeling, model space analysis, and association rule analysis to extract the relationship between structural deformation and gold mineralization. The Apriori algorithm with spatial constraints is used to quantify the favorable mineralization sites in the Jiaojia gold field using different combinations of ore-controlling indicators. The first favorable mineralization site has a 44% probability of mineralization and is primarily located in segments of the fault footwall within 25 m of the fault buffer where the transition from steep to gentle occurs (∼1–24). Its uniform distribution indicates that the ore-bearing space near the main fault plane is relatively wide, and hydrothermal diffusion is relatively uniform. Site No. 2 has a 45% probability of mineralization and is located in convex segments (6–35 m) between 25 and 55 m of the fault footwall. The equidistant zonal distribution in this area indicates that secondary faults and fractures have facilitated the migration of hydrothermal fluids, resulting in the formation of extensive ore-bearing spaces. Site No. 3 sited in convex segments (∼0–6 m) distal to the fault footwall (∼55–515 m) of the fault buffer where the dip is gentle (∼30°–35°). The binary structure of differing dips formed by the intersection of steeply dipping orebodies and the slowly dipping orebodies in the central and southern parts of the Nanlü-Xinmu deposit exhibit the complex channel away from the main fault. In this study, the correlation between ore-controlling factors and mineralization in Jiaojia fold field is quantitatively expressed as favorable mineralization sites in the form of association rules, it would contribute to a deeper understanding of the underlying mechanisms governing the formation of structure-controlled orogenic gold deposits in the Jiaojia goldfield.
Evolutionary game and simulation analysis on quality supervision of low-carbon renovation of high-carbon emission enterprises under the reward and punishment mechanism
Authors: Weng Xiangjian , Yuan Chunhui , Hu Qihang , Xu Yuhe
Published: May 2023

From the perspective of multi-stakeholders, considering the rent-seeking phenomenon existing in the inspection and acceptance of low-carbon renovation under the government’s reward and punishment mechanism, this paper constructs a tripartite evolutionary game model of the government, third-party testing institutions, and high-carbon emission enterprises, analyzes the stability of the evolutionary strategies of all parties involved, and tests the influence of the reward and punishment mechanism, rent-seeking cost, and the cost difference between high carbon and low carbon on the choice of tripartite strategies through simulation. Finally, the stability of the equilibrium point in the tripartite game system is verified. The results show that 1 the government’s increase in the reward and punishment mechanism will promote the low-carbon renovation of high-carbon emission enterprises and the refusal to rent-seeking behavior choices, but the increase in incentives will weaken the government’s supervision; 2 the reward and punishment mechanism set by the government must meet the condition that the sum of the strength of the reward and punishment mechanism for each party is greater than its speculative income, so as to ensure the quality of low-carbon renovation of high-carbon emission enterprises; 3 the greater the rent-seeking cost paid by high-carbon emission enterprises, the more conducive it is to avoiding the unqualified low-carbon renovation of high-carbon emission enterprises; and 4 under the premise of certain sales revenue, the greater the cost difference between low-carbon production and high-carbon production, the lower the willingness of enterprises to low-carbon renovation. Therefore, reducing the production cost difference is an effective way to promote the low-carbon renovation of high-carbon emission enterprises.
Proteomic profiling of single extracellular vesicles reveals colocalization of SARS-CoV-2 with a CD81/integrin-rich EV subpopulation in sputum from COVID-19 severe patients
Authors: Sun Ruiting , Cai Yanling , Zhou Yumin , Bai Ge , Zhu Airu , Kong Panyue , Sun Jing , Li Yimin , Liu Yuefei , Liao Wenting , Liu Jiye , Cui Nan , Xiang Jinsheng , Li Bing , Zhao Jincun , Wu Di , Ran Pixin
Published: May 2023

Background

The global outbreak of COVID-19, and the limited availability of clinical treatments, forced researchers around the world to search for the pathogenesis and potential treatments. Understanding the pathogenesis of SARS-CoV-2 is crucial to respond better to the current coronavirus disease 2019 (COVID-19) pandemic.

Methods

We collected sputum samples from 20 COVID-19 patients and healthy controls. Transmission electron microscopy was used to observe the morphology of SARS-CoV-2. Extracellular vesicles (EVs) were isolated from sputum and the supernatant of VeroE6 cells, and were characterized by transmission electron microscopy, nanoparticle tracking analysis and Western-Blotting. Furthermore, a proximity barcoding assay was used to investigate immune-related proteins in single EV, and the relationship between EVs and SARS-CoV-2.

Result

Transmission electron microscopy images of SARS-COV-2 virus reveal EV-like vesicles around the virion, and western blot analysis of EVs extracted from the supernatant of SARS-COV-2-infected VeroE6 cells showed that they expressed SARS-COV-2 protein. These EVs have the infectivity of SARS-COV-2, and the addition can cause the infection and damage of normal VeroE6 cells. In addition, EVs derived from the sputum of patients infected with SARS-COV-2 expressed high levels of IL6 and TGF-β, which correlated strongly with expression of the SARS-CoV-2 N protein. Among 40 EV subpopulations identified, 18 differed significantly between patients and controls. The EV subpopulation regulated by CD81 was the most likely to correlate with changes in the pulmonary microenvironment after SARS-CoV-2 infection. Single extracellular vesicles in the sputum of COVID-19 patients harbor infection-mediated alterations in host and virus-derived proteins.

Conclusions

These results demonstrate that EVs derived from the sputum of patients participate in virus infection and immune responses. This study provides evidence of an association between EVs and SARS-CoV-2, providing insight into the possible pathogenesis of SARS-CoV-2 infection and the possibility of developing nanoparticle-based antiviral drugs.
Potential role of climate change on the spread of salmonid skin condition: the biogeochemical hypothesis on ulcerative dermal necrosis on the Słupia River - Poland
Authors: Stokowski Marcin , Sobiegraj Wojciech , Kulczykowska Ewa
Published: May 2023

Ulcerative dermal necrosis (UDN) it is an idiopathic condition of fish skin that has been reported in Europe since 1820. UDN affects primarily an epidermal and dermal layer of the skin lesion, which in the early stages, occurs in the head area of migratory adult salmonids entering freshwater for upstream river migration. Studies show that acid-base water properties in estuaries are exceptionally dynamic, which results from the variability of the CO2 system. The carbonate system is shaped by the net effect of mineralization and primary production enhanced by: i) the constant inflow of nutrients and organic matter from the land and ii) the horizontal and vertical mixing of the two end-members of the total alkalinity, dissolved organic carbon and pCO2; both cause high acid-base gradients between the river and the ocean. Climate change affects the biogeochemical characteristics of estuaries. We show a strong positive correlation between local temperature anomalies along the Polish coast and the occurrence of UDN in Salmo trutta sp. spawners in the Słupia River, Poland. The results suggest that the biogeochemical processes associated with climate change may be at least one component of the UDN aetiology. They also highlight the need for systematic monitoring to understand these processes and their consequences. It is crucial for restoring and further preserving sustainability in the coastal system, which involves marine life and human well-being. Furthermore, salmonids are valuable commercial fish. Thus any health issues may have a profound effect on fisheries, local communities and the fish market in general.
Study on the inactivation and reactivation mechanism of pathogenic bacteria in aquaculture by UVC-LED
Authors: Zhang Weixiao , Huang Ruipin , Zhang Tao , Wang Baolong , Li Na , Sun Yan , Ma He , Zhang Qian , Zhang Junxin , Liu Ying
Published: May 2023

Ultraviolet disinfection is an important method for controlling the large-scale outbreaks of diseases in aquaculture. As a novel and promising light source, ultraviolet light-emitting diode (UV-LED) has the advantages of safety, high efficiency and no environmental pollution risks. However, it remains unclear whether UV-LEDs can replace traditional UV light sources for aquaculture water treatment processes. Present study aimed to investigate the efficacy of UVC-LEDs (265 nm) on pathogenic bacteria, specifically Aeromonas salmonicida and Escherichia coli. The effects of UVC-LED dose, light conditions, and temperature on bacterial reactivation were also investigated. The results showed that exposure to UVC-LED effectively inactivated both types of bacteria. To achieve 4.5-log inactivation of A. salmonicida and E. coli, 24 mJ/cm2 and 28 mJ/cm2 UVC-LED irradiation were required, and the inactivation rate increased with increasing UVC-LED fluence. Both A. salmonicida and E. coli were revived after UVC-LED disinfection, and photoreactivation was significantly higher than dark reactivation. Bacterial reactivation rate due to high-dose UVC-LED treatment was significantly lower than that of low-dose. After 72 h of reactivation, photoreactivation and dark reactivation rates were 1 ± 0.4% and 2.2 ± 0.2%for A. salmonicida, and 0.02% and 0% for E. coli, respectively. Besides, the photoreactivation rates for the two bacteria exhibited different correlations with temperature. The highest photoreactivation rate for A. salmonicida was 68.7 ± 4% at 20°C, while the highest photoreactivation rate for E. coli was 53.98 ± 2.9% at 15°C for 48 h. This study reveals the rapid and efficient inactivation of bacteria by UVC-LED, and elucidates the mechanism and influencing factors for inactivation and reactivation by UVC-LED. The study also highlights that adequate UVC-LED irradiation and avoidance of visible light after UVC-LED disinfection can effectively inhibit bacterial reactivation. Our findings form a reference for the design and operation of UV disinfection in aquaculture.
Growth of marine biofilms and macrofouling organisms on biocide-infused, 3D-printed thermoplastics
Authors: Shimeta Jeff , Wilding-McBride Gemma , Bott Nathan J. , Piola Richard , Santander Rene , Leary Martin , Scardino Andrew J.
Published: May 2023

3D printing has become widely used to rapidly prototype and manufacture novel or bespoke objects or replacement components in a wide range of marine industries, engineering, and research. 3D-printed objects are subject to marine biofouling, impacting their operation and longevity. Application of antifouling paints or coatings adds costly and time-consuming steps and may interfere with the function of fine surface features, counteracting some of the benefits of 3D-printing technology. We measured the antifouling performance of two 3D-printing thermoplastics embedded with antifouling biocides to create 3D-printed materials with inherent antifouling properties: 1) polycaprolactone (PCL) mixed with the organic biocide dichlorooctylisothiazolinone (DCOIT) and extruded as 3D-printing filament, and 2) a commercial polylactic acid (PLA) 3D-printing filament with embedded copper powder. Settlement plates printed from these thermoplastics (“PCL-DCOIT” and “PLA-Cu”, respectively) and deployed in temperate, coastal marine water for 17 weeks during summer remained free of macrofouling. A biofilm developed, and 16S and 18S rRNA metabarcoding analyses revealed that early stage biofilms (at 5 and 12 weeks) had dramatically altered assemblage structures of both prokaryotes and eukaryotes compared to natural biofilms. The assemblage on PCL-DCOIT had reduced microbial diversity, strong dominance of Proteobacteria and chlorophytes, and almost complete absence of Flavobacteriia, Cyanobacteria, and diatoms. In contrast, the biofilm on PLA-Cu had a dominance of Flavobacteriia over Proteobacteria, and resistance to chlorophytes, yet similar to PCL-DCOIT it resisted Cyanobacteria and diatoms. Such alterations to biofilm microbial assemblages could influence microbial dynamics, biofilm growth, and settlement cues to which biofouler propagules respond. At 17 weeks, the two biocide-embedded thermoplastics completely resisted macrofouling, equally well as three commercial antifouling coatings (Intercept 8500, Hempaguard X7, Hempasil X3); however, PCL-DCOIT was more extensively covered by a microalgal film (79%, evidently chlorophytes) than were the commercial coatings, and PLA-Cu had the most settled detritus (100% cover). Biofilm assemblages on the commercial coatings were investigated for comparison, with PCL-DCOIT standing out due to its almost complete resistance to Flavobacteriia. Thermoplastic 3D-printing filaments with embedded biocides show promise for producing 3D-printed objects with inherent antifouling properties, avoiding or lessening the need to apply antifouling coatings, and possibly extending their service lifetime.
Comparison of short and long forms of the Flinders program of chronic disease SELF-management for participants starting SGLT-2 inhibitors for congestive heart failure (SELFMAN-HF): protocol for a prospective, observational study
Authors: Iyngkaran Pupalan , Hanna Fahad , Andrew Sharon , Horowitz John David , Battersby Malcolm , De Courten Maximilian Pangratius
Published: May 2023

Introduction

Congestive heart failure (CHF) causes significant morbidity and mortality. It is an epidemic, and costs are escalating. CHF is a chronic disease whose trajectory includes stable phases, periods of decompensation, and finally palliation. Health services and medical therapies must match the various patient needs. Chronic disease self-management (CDSM) programmes that are patient-focused, identify problems and set actionable goals that appear as a logical, cost-friendly method to navigate patient journeys. There have been challenges in standardising and implementing CHF programmes.

Methods and analysis

SELFMAN-HF is a prospective, observational study to evaluate the feasibility and validity of the SCRinHF tool, a one-page self-management and readmission risk prediction tool for CHF, with an established, comprehensive CDSM tool. Eligible patients will have CHF with left ventricular ejection fraction <40% and commenced sodium glucose co-transporter-2 inhibitors (SGLT2-i) within 6 months of recruitment. The primary endpoint is the 80% concordance in readmission risk predicted by the SCRinHF tool. The study will recruit >40 patients and is expected to last 18 months.

Ethics and dissemination

This study has been approved by the St Vincent’s ethics committee (approval no. LRR 177/21). All participants will complete a written informed consent prior to enrolment in the study. The study results will be disseminated widely via local and international health conferences and peer-reviewed publications.
Positive- vs. negative-pressure extubation technique: a scoping review
Authors: Liu Jing , Li Fang , Qi Xiangyang , Zhuang Xin , Cui Zhaomei
Published: May 2023

Objectives

This review aimed to summarize the recent literature on positive-pressure extubation.

Design

A scoping review was conducted under the framework of the Joanna Briggs Institute.

Data sources

Web of Science, PubMed, Ovid, Cumulative Index to Nursing & Allied Health, EBSCO, Cochrane Library, Wan Fang Data, China National Knowledge Infrastructure, and China Biology Medicine databases were searched for studies on adults and children.

Study selection

All articles describing the use of positive-pressure extubation were considered eligible for inclusion. The exclusion criteria were articles not available in English or Chinese, and those without full text available.

Data extraction and synthesis

The database searches identified 8,381 articles, 15 of which could be included in this review, with an aggregated patient number of 1,544. Vital signs, including mean arterial pressure, heart rate, R-R interval, and SpO2 before and after extubation; blood gas analysis indexes, including pH, oxygen saturation, PaO2, and PaCO2 before and after extubation; and incidence of respiratory complications, including bronchospasm, laryngeal edema, aspiration atelectasis, hypoxemia, and hypercapnia, were reported in the included studies.

Results

The majority of these studies reported that the positive-pressure extubation technique can maintain stable vital signs and blood gas analysis indices as well as prevent complications during the peri-extubation period.

Conclusions

The positive-pressure extubation technique has a safety performance similar to that of the traditional negative-pressure extubation technique and may lead to better clinical outcomes, including stable vital signs, arterial blood gas analysis, and a lower incidence of respiratory complications.
Two novel Planococcus species isolated from baijiu pit mud with potential application in brewing
Authors: Hao Shuyue , Ren Qing , Wang Jiaxuan , Li Liya , Huang Mingquan
Published: May 2023

Two novel Gram-positive bacteria, designated strains REN8T and REN14T, were isolated from baijiu pit mud in Sichuan Province, China. REN8T achieved the best growth at 37°C, a pH of 8.0, and a NaCl concentration of 2%, while REN14T displayed optimal growth at 37°C, a pH of 6.0, and a NaCl concentration of 1%. 16S rRNA and genomic phylogenetic analysis showed that REN8T and REN14T were clustered with the genus Planococcus. The genomic DNA G + C contents of REN8T and REN14T were 46.7 and 45.1 mol%, respectively. The dDDH and ANI values were 24.5 and 80.43% between REN8T and P. salinarum (the most closely related type strain) and 25.1 and 82.42% between REN14T and P. soli (the most closely related type strain). Genomic analysis showed that several carbohydrate-active enzymes and secondary metabolite gene clusters existed in REN8T and REN14T. Chemotaxonomic characteristics of REN8T and REN14T included major fatty acids, predominant menaquinones, and polar lipids, all of which were consistent with the genus Planococcus. Based on the polyphasic taxonomic method, these two strains represent two novel species of the genus Planococcus; the name Planococcus beigongshangi sp. nov. is proposed for the type strain REN8T (=JCM 33964T = GDMCC 1.2213T), and the name Planococcus beijingensis sp. nov. is proposed for the type strain REN14T (=JCM 34410T = GDMCC 1.2209T). The addition of REN8T and REN14T might improve the quality of huangjiu by considerably increasing the amino acid nitrogen content and acidity and decreasing the bioamine content, with no significant change in alcohol content.
Administration of Bifidobacterium animalis subsp. lactis strain BB-12® in healthy children: characterization, functional composition, and metabolism of the gut microbiome
Authors: Vizioli Carlotta , Jaime-Lara Rosario , Daniel Scott G. , Franks Alexis , Diallo Ana F. , Bittinger Kyle , Tan Tina P. , Merenstein Daniel J. , Brooks Brianna , Joseph Paule V. , Maki Katherine A.
Published: May 2023

Introduction

The consumption of probiotics may influence children’s gut microbiome and metabolome, which may reflect shifts in gut microbial diversity composition and metabolism. These potential changes might have a beneficial impact on health. However, there is a lack of evidence investigating the effect of probiotics on the gut microbiome and metabolome of children. We aimed to examine the potential impact of a two (Streptococcus thermophilus and Lactobacillus delbrueckii; S2) vs. three (S2 + Bifidobacterium animalis subsp. lactis strain BB-12) strain-supplemented yogurt.

Methods

Included in this study were 59 participants, aged one to five years old, recruited to phase I of a double-blinded, randomized controlled trial. Fecal samples were collected at baseline, after the intervention, and at twenty days post-intervention discontinuation, and untargeted metabolomics and shotgun metagenomics were performed.

Results

Shotgun metagenomics and metabolomic analyses showed no global changes in either intervention group’s gut microbiome alpha or beta diversity indices, except for a lower microbial diversity in the S2 + BB12 group at Day 30. The relative abundance of the two and three intervention bacteria increased in the S2 and S2 + BB12 groups, respectively, from Day 0 to Day 10. In the S2 + BB12 group, the abundance of several fecal metabolites increased at Day 10, including alanine, glycine, lysine, phenylalanine, serine, and valine. These fecal metabolite changes did not occur in the S2 group.

Discussion

In conclusion, there were were no significant differences in the global metagenomic or metabolomic profiles between healthy children receiving two (S2) vs. three (S2 + BB12) probiotic strains for 10 days. Nevertheless, we observed a significant increase (Day 0 to Day 10) in the relative abundance of the two and three probiotics administered in the S2 and S2 + BB12 groups, respectively, indicating the intervention had a measurable impact on the bacteria of interest in the gut microbiome. Future research using longer probiotic intervention durations and in children at risk for gastrointestinal disorders may elucidate if functional metabolite changes confer a protective gastrointestinal effect.
Effects of biochar in combination with varied N inputs on grain yield, N uptake, NH3 volatilization, and N2O emission in paddy soil
Authors: Yi Zhenghua , Jeyakumar Paramsothy , Yin Chengcheng , Sun Haijun
Published: May 2023

Biochar application can improve crop yield, reduce ammonia (NH3) volatilization and nitrous oxide (N2O) emission from farmland. We here conducted a pot experiment to compare the effects of biochar application on rice yield, nitrogen (N) uptake, NH3 and N2O losses in paddy soil with low, medium, and high N inputs at 160 kg/ha, 200 kg/ha and 240 kg/ha, respectively. The results showed that: (1) Biochar significantly increased the rice grain yield at medium (200 kg/ha) and high (240 kg/ha) N inputs by 56.4 and 70.5%, respectively. The way to increase yield was to increase the rice N uptake, rice panicle number per pot and 1,000 grain weight by 78.5–96.5%, 6–16% and 4.4–6.1%, respectively; (2) Under low (160 kg/ha) N input, adding biochar effectively reduced the NH3 volatilization by 31.6% in rice season. The decreases of pH value and NH4+-N content in surface water, and the increases of the abundance of NH4+-N oxidizing archaea and bacteria (AOA and AOB) communities contributed to the reduction of NH3 volatilization following the biochar application; (3) Under same N input levels, the total N2O emission in rice season decreased by 43.3–73.9% after biochar addition. The decreases of nirK and nirS gene abundances but the increases of nosZ gene abundance are the main mechanisms for biochar application to reduce N2O emissions. Based on the results of the current study, adding biochar at medium (200 kg/ha) N level (N200 + BC) is the best treatment to synchronically reduce NH3 and N2O losses, improve grain yield, and reduce fertilizer application in rice production system.
Zonation of the active methane-cycling community in deep subsurface sediments of the Peru trench
Authors: Lever Mark A. , Alperin Marc J. , Hinrichs Kai-Uwe , Teske Andreas
Published: May 2023

The production and anaerobic oxidation of methane (AOM) by microorganisms is widespread in organic-rich deep subseafloor sediments. Yet, the organisms that carry out these processes remain largely unknown. Here we identify members of the methane-cycling microbial community in deep subsurface, hydrate-containing sediments of the Peru Trench by targeting functional genes of the alpha subunit of methyl coenzyme M reductase (mcrA). The mcrA profile reveals a distinct community zonation that partially matches the zonation of methane oxidizing and –producing activity inferred from sulfate and methane concentrations and carbon-isotopic compositions of methane and dissolved inorganic carbon (DIC). McrA appears absent from sulfate-rich sediments that are devoid of methane, but mcrA sequences belonging to putatively methane-oxidizing ANME-1a-b occur from the zone of methane oxidation to several meters into the methanogenesis zone. A sister group of ANME-1a-b, referred to as ANME-1d, and members of putatively aceticlastic Methanothrix (formerly Methanosaeta) occur throughout the remaining methanogenesis zone. Analyses of 16S rRNA and mcrA-mRNA indicate that the methane-cycling community is alive throughout (rRNA to 230 mbsf) and active in at least parts of the sediment column (mRNA at 44 mbsf). Carbon-isotopic depletions of methane relative to DIC (−80 to −86‰) suggest mostly methane production by CO2 reduction and thus seem at odds with the widespread detection of ANME-1 and Methanothrix. We explain this apparent contradiction based on recent insights into the metabolisms of both ANME-1 and Methanothricaceae, which indicate the potential for methanogenetic growth by CO2 reduction in both groups.
Characterization and genomic study of EJP2, a novel jumbo phage targeting antimicrobial resistant Escherichia coli
Authors: Jo Dohyeong , Kim Hyeongsoon , Lee Yoona , Kim Jinshil , Ryu Sangryeol
Published: May 2023

The emergence of antimicrobial resistance (AMR)Escherichia colihas noticeably increased in recent years worldwide and causes serious public health concerns. As alternatives to antibiotics, bacteriophages are regarded as promising antimicrobial agents. In this study, we isolated and characterized a novel jumbo phage EJP2 that specifically targets AMRE. colistrains. EJP2 belonged to theMyoviridaefamily with an icosahedral head (120.9 ± 2.9 nm) and a non-contractile tail (111.1 ± 0.6 nm), and contained 349,185 bp double-stranded DNA genome with 540 putative ORFs, suggesting that EJP2 could be classified as jumbo phage. The functions of genes identified in EJP2 genome were mainly related to nucleotide metabolism, DNA replication, and recombination. Comparative genomic analysis revealed that EJP2 was categorized in the group of Rak2-related virus and presented low sequence similarity at the nucleotide and amino acid level compared to otherE. colijumbo phages. EJP2 had a broad host spectrum against AMRE. colias well as pathogenicE. coliand recognized LPS as a receptor for infection. Moreover, EJP2 treatment could remove over 80% of AMRE. colibiofilms on 96-well polystyrene, and exhibit synergistic antimicrobial activity with cefotaxime against AMRE. coli. These results suggest that jumbo phage EJP2 could be used as a potential biocontrol agent to combat the AMR issue in food processing and clinical environments.
Exploring the shared gene signatures of smoking-related osteoporosis and chronic obstructive pulmonary disease using machine learning algorithms
Authors: Wang Haotian , Li Shaoshuo , Chen Baixing , Wu Mao , Yin Heng , Shao Yang , Wang Jianwei
Published: May 2023

Objectives: Cigarette smoking has been recognized as a predisposing factor for both osteoporosis (OP) and chronic obstructive pulmonary disease (COPD). This study aimed to investigate the shared gene signatures affected by cigarette smoking in OP and COPD through gene expression profiling.

Materials and methods: Microarray datasets (GSE11784, GSE13850, GSE10006, and GSE103174) were obtained from Gene Expression Omnibus (GEO) and analyzed for differentially expressed genes (DEGs) and weighted gene co-expression network analysis (WGCNA). Least absolute shrinkage and selection operator (LASSO) regression method and a random forest (RF) machine learning algorithm were used to identify candidate biomarkers. The diagnostic value of the method was assessed using logistic regression and receiver operating characteristic (ROC) curve analysis. Finally, immune cell infiltration was analyzed to identify dysregulated immune cells in cigarette smoking-induced COPD.

Results: In the smoking-related OP and COPD datasets, 2858 and 280 DEGs were identified, respectively. WGCNA revealed 982 genes strongly correlated with smoking-related OP, of which 32 overlapped with the hub genes of COPD. Gene Ontology (GO) enrichment analysis showed that the overlapping genes were enriched in the immune system category. Using LASSO regression and RF machine learning, six candidate genes were identified, and a logistic regression model was constructed, which had high diagnostic values for both the training set and external validation datasets. The area under the curves (AUCs) were 0.83 and 0.99, respectively. Immune cell infiltration analysis revealed dysregulation in several immune cells, and six immune-associated genes were identified for smoking-related OP and COPD, namely, mucosa-associated lymphoid tissue lymphoma translocation protein 1 (MALT1), tissue-type plasminogen activator (PLAT), sodium channel 1 subunit alpha (SCNN1A), sine oculis homeobox 3 (SIX3), sperm-associated antigen 9 (SPAG9), and vacuolar protein sorting 35 (VPS35).

Conclusion: The findings suggest that immune cell infiltration profiles play a significant role in the shared pathogenesis of smoking-related OP and COPD. The results could provide valuable insights for developing novel therapeutic strategies for managing these disorders, as well as shedding light on their pathogenesis.
A Y374X TDP43 truncation leads to an altered metabolic profile in amyotrophic lateral sclerosis fibroblasts driven by pyruvate and TCA cycle intermediate alterations
Authors: Allen Scott P. , Al Sultan Afnan , Kabucho Kibirige Elaine , Tonkiss Erin , Hamer Keaton J. , Castelli Lydia M. , Lin Ya-Hui , Roscoe Sarah , Stefanidis Nikolaos , Mead Richard J. , Highley J. Robin , Cooper-Knock Johnathan , Hautbergue Guillaume M. , Heath Paul R. , Kirby Janine , Shaw Pamela J.
Published: May 2023

A p.Y374X truncation in TARDBP was recently shown to reduce expression of TDP43 in fibroblasts isolated from ALS cases. In this follow up study focused on assessing the downstream phenotypic consequences of loss of TDP43 in the context of the truncation, we have shown a striking effect on the fibroblast metabolic profile. Phenotypic metabolic screening uncovered a distinct metabolic profile in TDP43-Y374X fibroblasts compared to controls, which was driven by alterations in key metabolic checkpoint intermediates including pyruvate, alpha-ketoglutarate and succinate. These metabolic alterations were confirmed using transcriptomics and bioenergetic flux analysis. These data suggest that TDP43 truncation directly compromises glycolytic and mitochondrial function, identifying potential therapeutic targets for mitigating the effects of TDP43-Y374X truncation.
Social support and cognitive function in Chinese older adults who experienced depressive symptoms: is there an age difference?
Authors: Jing Yurong , Wang Wei , Peng Wenjia , Wang Meng , Chen Xiaoli , Liu Xinya , Wang Pengfei , Yan Fei , Yang Yinghua , Wang Xinguo , Sun Shuangyuan , Ruan Ye , Wang Ying
Published: May 2023

Objective

This study examined the moderating effect of overall social support and the different types of social support on cognitive functioning in depressed older adults. We also investigated whether the moderating effect varied according to age.

Methods

A total of 2,500 older adults (≥60 years old) from Shanghai, China were enrolled using a multistage cluster sampling method. Weighted linear regression and multiple linear regression was utilized to analyze the moderating effect of social support on the relationship between depressive symptoms and cognitive function and to explore its differences in those aged 60–69, 70–79, and 80 years and above.

Results

After adjusting for covariates, the results indicated that overall social support (β = 0.091, p = 0.043) and support utilization (β = 0.213, p < 0.001) moderated the relationship between depressive symptoms and cognitive function. Support utilization reduced the possibility of the cognitive decline in depressed older adults aged 60–69 years (β = 0.310, p  < 0.001) and 80 years and above (β = 0.199, p  < 0.001), while objective support increased the possibility of cognitive decline in depressed older people aged 70–79 years (β = −0.189, p  < 0.001).

Conclusion

Our findings highlight the buffering effects of support utilization on cognitive decline in depressed older adults. We suggest that age-specific measures should be taken when providing social support to depressed older adults in order to reduce the deterioration of cognitive function.
Relation of early-stage renal insufficiency and cardiac structure and function in a large population of asymptomatic Asians: a cross-sectional cohort analysis
Authors: Wu Pei-Chen , Sung Kuo-Tzu , Lin Jiun-Lu , Hung Ta-Chuan , Lai Yau-Huei , Su Cheng-Huang , Yeh Hung-I. , Wu Chih-Jen , Hung Chung-Lieh
Published: May 2023

Background

Few studies have addressed early-stage kidney disease and preclinical cardiac structural and functional abnormalities from a large-scale Asian population. Further, the extent to which measures of myocardial function and whether these associations may vary by testing various formulas of renal insufficiency remains largely unexplored.

Objective

To explore the associations among renal function, proteinuria, and left ventricular (LV) structural and diastolic functional alterations.

Design

A cross-sectional, retrospective cohort study.

Setting

Registered data from a cardiovascular health screening program at MacKay Memorial Hospital from June 2009 to December 2012.

Participants

Asymptomatic individuals.

Measurements

Renal function was evaluated in terms of estimated glomerular filtration rate (eGFR) by both MDRD and CKD-EPI formulas and severity of proteinuria, which were further related to cardiac structure, diastolic function (including LV e’ by tissue Doppler), and circulating N-terminal pro-brain natriuretic peptide (NT-proBNP) level.

Results

Among 4942 participants (65.8% men, mean age 49.4 ± 11.2 years), the mean CKD-EPI/MDRD eGFR was 90.6 ± 15.7 and 88.5 ± 16.9 ml/min/1.73m2, respectively. Lower eGFR, estimated either by the MDRD or CKD-EPI method, and higher proteinuria were significantly associated with lower LV e’ and higher NT-proBNP (all p<0.05) even after adjusting for clinical covariates. In general, lower eGFR estimated by CKD-EPI and MDRD displayed similar impacts on worsening e’ and NT-proBNP, rather than E/e’, in multivariate models. Finally, lower LV e’ or higher composite diastolic score, rather than E/e’, demonstrated remarkable interaction with eGFR level estimated by either CKD-EPI or MDRD on circulating NT-proBNP level (p interaction <0.05).

Limitations

Proteinuria was estimated using a urine dipstick rather than more accurately by the urine protein-to-creatinine ratio. Also, pertaining drug history and clinical hard outcomes were lacking.

Conclusion

Both clinical estimate of renal insufficiency by eGFR or proteinuria, even in a relatively early clinical stage, were tightly linked to impaired cardiac diastolic relaxation and circulating NT-proBNP level. Elevation of NT-proBNP with worsening renal function may be influenced by impaired myocardial relaxation.
Inflammatory cytokines associated with mild traumatic brain injury and clinical outcomes: a systematic review and meta-analysis
Authors: Malik Shazia , Alnaji Omar , Malik Mahnoor , Gambale Teresa , Farrokhyar Forough , Rathbone Michel P.
Published: May 2023

Mild traumatic brain injuries (mTBIs) trigger a neuroinflammatory response, which leads to perturbations in the levels of inflammatory cytokines, resulting in a distinctive profile. A systematic review and meta-analysis were conducted to synthesize data related to levels of inflammatory cytokines in patients with mTBI. The electronic databases EMBASE, MEDLINE, and PUBMED were searched from January 2014 to December 12, 2021. A total of 5,138 articles were screened using a systematic approach based on the PRISMA and R-AMSTAR guidelines. Of these articles, 174 were selected for full-text review and 26 were included in the final analysis. The results of this study demonstrate that within 24 hours, patients with mTBI have significantly higher levels of Interleukin-6 (IL-6), Interleukin-1 Receptor Antagonist (IL-1RA), and Interferon-γ (IFN-γ) in blood, compared to healthy controls in majority of the included studies. Similarly one week following the injury, patients with mTBI have higher circulatory levels of Monocyte Chemoattractant Protein-1/C-C Motif Chemokine Ligand 2 (MCP-1/CCL2), compared to healthy controls in majority of the included studies. The results of the meta-analysis also confirmed these findings by demonstrating significantly elevated blood levels of IL-6, MCP-1/CCL2, and Interleukin-1 beta (IL-1β) in the mTBI population compared to healthy controls (p < 0.0001), particularly in the acute stages (<7 days). Furthermore, it was found that IL-6, Tumor Necrosis Factor-alpha (TNF-α), IL-1RA, IL-10, and MCP-1/CCL2 were associated with poor clinical outcomes following the mTBI. Finally, this research highlights the lack of consensus in the methodology of mTBI studies that measure inflammatory cytokines in the blood, and also provides direction for future mTBI research.