bluuebunny/crossref_metadata_2025 huggingface dataset:
Multi-habitat seascape restoration: optimising marine restoration for coastal repair and social benefit
Authors: McAfee Dominic , Reis-Santos Patrick , Jones Alice R. , Gillanders Bronwyn M. , Mellin Camille , Nagelkerken Ivan , Nursey-Bray Melissa J. , Baring Ryan , da Silva Graziela Miot , Tanner Jason E. , Connell Sean D.
Published: August 2022

Marine ecosystem restoration is fast becoming the primary tool for repairing the socio-ecological functions and economic benefits of coastal ecosystems. Healthy seascapes are characterized by many interacting species and intermingled habitats (e.g., seagrass, kelp, shellfish, sedimentary) that co-create ecological functions of substantial socio-economic value. These co-created functions not only build stability and resilience at seascape scales, but synergistically combine to enhance ecological productivity that is greater than the sum of the individual habitats. Yet, restoration practice is dominated by single-habitat approaches underpinned by single-species monocultures, potentially limiting the range of benefits that restoration can provide. We propose that for ecosystem restoration to meet its full potential in delivering socio-ecological benefits that are resilient to environmental change, restoration practices should plan beyond single-species and single-habitats to a multi-habitat seascape. Where multiple habitats are co-restored, their positive interactions mutually benefit each other to stabilize and even accelerate ecosystem recovery; such as co-restored shellfish and kelp forests on constructed reefs, which combine to stabilize sediment for seagrass recovery. As fisheries scientists and managers, food and social scientists, and ecologists and oceanographers, we describe multi-habitat marine restoration activities that are readily achievable and provide a vision for the diverse socio-ecological, economic, and culture benefits that may emerge from future seascape-level repair.
Using larval connectivity to inform conservation management of the endemic and threatened Atlantic mud-piddock (Barnea truncata) in the Minas Basin Canada
Authors: Krumhansl Kira A. , Gentleman Wendy C. , Wu Yongsheng , Wang Xiaoyi , DiBacco Claudio
Published: August 2022

Understanding metapopulation dynamics is critical for effective species conservation, but they are not always considered for marine species due to difficulties in assessing connectivity in marine environments. This is particularly true for species that are rare or threatened, as demographic and life history data are usually sparse. We employ Lagrangian Particle Tracking (LPT) to assess metapopulation dynamics and inform spatial management measures for the Atlantic Mud Piddock (AMP; Barnea truncata), a poorly studied and threatened marine bivalve mollusk in Canada, whose distribution in the country is limited to a single population in the Minas Basin, Nova Scotia. In a series of simulations designed to account for uncertainty in biological attributes of AMP, we identified that sub-populations along the southern coastline of the Minas Basin were the most strongly connected to other sub-populations by acting as the greatest sources and sinks of simulated larvae. Propagules released from the Minas Basin dispersed as far as the US coast of the Gulf of Maine, which harbors the closest known population of AMP outside of the Minas Basin. However, there was no exchange of larvae in the opposite direction, from the US population of AMP in the Gulf of Maine to the Minas Basin. These results suggest that sub-populations in the Minas Basin are self-sustaining (i.e., sub-populations that exchange larvae and ultimately act as a meta-population), supporting the need to protect critical source sites along the southern coastline for the regional persistence of this species. More generally, these results show how LPT outputs can be directly applied to conservation planning, and used to identify key knowledge gaps to address with future work to reduce uncertainty in model predictions.
Graphical Analysis of A Marine Plankton Community Reveals Spatial, Temporal, and Niche Structure of Sub-Communities
Authors: Siddons Joseph T. , Irwin Andrew J. , Finkel Zoe V.
Published: August 2022

Species-rich communities are structured by environmental filtering and a multitude of associations including trophic, mutualistic, and antagonistic relationships. Graphs (networks) defined from correlations in presence or abundance data have the potential to identify this structure, but species with very high absence rates or abundances frequently near detection limits can result in biased retrieval of association graphs. Here we use graph clustering analysis to identify five sub-communities of plankton from the North Atlantic Ocean. We show how to mitigate the challenges of high absence rates and detection limits. The sub-communities are distinguished partially by their constituent functional groups: one group is dominated by diatoms and another by dinoflagellates, while the other three sub-communities are mixtures of phytoplankton and zooplankton. Diagnosing pairwise taxonomic associations and linking them to specific processes is challenging because of overlapping associations and complex graph topologies. Our approach presents a robust approach for identifying candidate associations among species through sub-community analysis and quantifying the aggregate strength of pairwise associations emerging in natural communities.
Identifying potential sources of iron-binding ligands in coastal Antarctic environments and the wider Southern Ocean
Authors: Smith Abigail J.R. , Nelson Talitha , Ratnarajah Lavenia , Genovese Cristina , Westwood Karen , Holmes Thomas M. , Corkill Matthew , Townsend Ashley T. , Bell Elanor , Wuttig Kathrin , Lannuzel Delphine
Published: August 2022

The availability of iron (Fe) to marine microbial communities is enhanced through complexation by ligands. In Fe limited environments, measuring the distribution and identifying the likely sources of ligands is therefore central to understanding the drivers of marine productivity. Antarctic coastal marine environments support highly productive ecosystems and are influenced by numerous sources of ligands, the magnitude of which varies both spatially and seasonally. Using competitive ligand exchange adsorptive cathodic stripping voltammetry (CLE-AdCSV) with 2-(2-thiazolylazo)-p-cresol (TAC) as a competing artificial ligand, this study investigates Fe-binding ligands (FeL) across the continental shelf break in the Mertz Glacier Region, East Antarctica (64 - 67°S; 138 - 154°E) during austral summer of 2019. The average FeL concentration was 0.86 ± 0.5 nM Eq Fe, with strong conditional stability constants (Log KFeL) averaging 23.1 ± 1.0. The strongest binding ligands were observed in modified circumpolar deep water (CDW), thought to be linked to bacterial Fe remineralisation and potential siderophore release. High proportions of excess unbound ligands (L’) were observed in surface waters, as a result of phytoplankton Fe uptake in the mixed layer and euphotic zone. However, FeL and L’ concentrations were greater at depth, suggesting ligands were supplied with dissolved Fe from upwelled CDW and particle remineralisation in benthic nepheloid layers over the shelf. Recent sea-ice melt appeared to support bacterial production in areas where Fe and ligands were exhausted. This study is included within our newly compiled Southern Ocean Ligand (SOLt) Collection, a database of publicly available Fe-binding ligand surveys performed south of 50°S. A review of the SOLt Collection brings attention to the paucity of ligand data collected along the East Antarctic coast and the difficulties in pinpointing sources of Fe and ligands in coastal environments. Elucidating poorly understood ligand sources is essential to predicting future Fe availability for microbial populations under rapid environmental change.
Molecular and biochemical effects on metabolism and immunity of Hyriopsis cumingii fed with four different microalgae
Authors: Sun Yu , Guo Kefan , Yu Xiaobo , Li Yanhong , Yao Weizhi , Wu Zhengli
Published: August 2022

Hyriopsis cumingii has attracted attention because of its pearl production performance and water purification capacity. Realizing sustainable industrialized culture of H. cumingii or applying it to bivalve biomanipulation for controlling water eutrophication needs urgent studies about the selection of suitable algae and the effects of different microalgae on mussel physiology. To contrast molecular and biochemical effects of high-quality microalgal diets (Chlorella vulgaris, Navicula pelliculosa, and Cyclotella sp.) with toxic Microcystis aeruginosa on metabolism and immune physiology of H. cumingii, levels of related enzymes and genes were analyzed during the 28-day exposure period. Results showed that the Cyclotella sp. diet could significantly (p < 0.05) maintain higher levels of metabolic enzymes (glutamic oxaloacetate transaminase (GOT), glutamic pyruvate transaminase (GPT), pyruvate kinase (PK), and hexokinase (HK)) and genes (CPT1 and LDLR). C. vulgaris and N. pelliculosa treatments significantly (p < 0.05) reduced activities of these metabolic parameters. The M. aeruginosa treatment significantly (p < 0.05) enhanced levels of immune enzymes (alkaline phosphatase (AKP), superoxide dismutase (SOD), and catalase (CAT)) and genes (HcIL-17 and IAP) on day 1 or 7, and there was a significant (p < 0.05) reduction on day 28. Results suggested that Cyclotella sp. was the suitable algae for H. cumingii, followed by C. vulgaris and N. pelliculosa, and toxic algae caused metabolic disorders, immune injury, and poor physiological status. The study has practical significance in the sustainable cultivation of H. cumingii and provides a theoretical basis for bivalve biomanipulation in eutrophic water.
Effect of laser scanning speed on microstructure and mechanical properties of SLM porous Ti-5Al-5V-5Mo-3Cr-1Fe alloy
Authors: Yuan Wei , Zhao Xiaoli , Li Shujun , Zhu Yue
Published: August 2022

In this study, porous Ti-55531(Fe) was fabricated by selective laser melting (SLM) with different laser scanning speeds. The microstructures, surface morphology, inner defects, porosity, microhardness, and compressive behaviors were studied. The variation of lattice constant and hardness were analyzed. The results show that all the specimens have a density of ∼1 g/cm3, and a Vicker’s hardness with a range of 280–320 Hv0.1. The porosity of the SLM-produced materials is greater than the designed value (77%) and increases from 77.33% to 82.33% with the increase of laser scanning speed from 500 mm/s to 1,500 mm/s. Continuous irregular columnar dendrites, a large number of gas-induced defects with small size between 20 and 60 μm and a deep molten pool form in the specimens fabricated with a laser scanning speed less than 1,000 mm/s. Some defects, elongated voids and interrupted columnar dendrites are identified in the specimens fabricated with the laser scanning speed more than 1,000 mm/s caused by the insufficient input energy. All specimens with different laser scanning speeds show the single ß phase patterns. The compressive strength of the specimens with the laser scanning speed of 500 mm/s is maintained at 32 MPa and the compressive strength decreases with the increase of laser scanning speed. The specimens with a scanning speed of 500 mm/s present the best mechanical properties and surface quality.
Examining distractor qualities of pediatrics subject tests from a national assessment
Authors: Pan Qianqian , Jiang Zhehan
Published: August 2022

Background

Analyzing distractor qualities of a pediatrics subject test in a national-level examination is vital in developing high-quality items for the discipline. Yet traditional approaches focus on key answers only and therefore are less informative. The number of distractors can also be parsimonized to improve the item development.

Materials and methods

From a pediatrics subject test at the national level, raw responses of 44,332 examines to nineteen multiple-choice questions were analyzed, such that the distractor qualities were evaluated via traditional and advanced methods such as canonical correlation index. Additionally, a simulation study was conducted to investigate the impact of eliminating distractor numbers on reliability.

Results

The traditional item analysis showed that most items had acceptable psychometric properties, and two items were flagged for low item difficulty and discrimination. Distractor analysis showed that about one-third of items had poorly functioning distractors based on relatively a low choice frequency (<5%) and a small effect size of distractor discrimination. The simulation study also confirmed that shrinking distractor numbers to 4 was viable.

Conclusions

Integrating multiple methods, especially the advanced ones, provides comprehensive evaluations of the item quality. Simulations can help re-consider the decision to set distractor numbers for cost-effectiveness. These proposed methods can improve further development of the pediatrics subject test.
Exclusion of older adults from clinical trials in cancer-related pain
Authors: Krysa Krzysztof , Kowalczyk Ewa , Borysowski Jan , Lachota Mieszko , Pasierski Tomasz
Published: August 2022

Pain is one of the most common symptoms in cancer patients including older adults. The objective of this study was to evaluate the enrollment criteria that can limit the inclusion of older adults in clinical trials concerning cancer-related pain (CRP). The study included 356 trials registered with ClinicalTrials.gov. Our primary outcome measures were the proportion of trials that excluded patients based on upper age limits (80 years of age or less), strict organ-specific exclusion criteria, broad and imprecise criteria, and inadequate performance score. One hundred and twenty-six trials (35.4%) had upper age limits. Strict exclusion criteria were used in 95 (26.7%) trials. Broad and imprecise exclusion criteria were listed in 57 (16.2%) trials. Low performance score was used as an exclusion criterion in 4 trials (1.1%). Overall, in 241 trials (67.7%) there was either an upper age limit or at least one strict or broad and imprecise exclusion criterion, or a criterion involving the performance status. The odds of excluding older adults were significantly higher in certain neoplasm types, study objectives, intervention types, and center locations. In conclusion, considerable proportion of recent clinical trials concerning CRP either explicitly exclude older adults or create high risk of such exclusion which substantially limits the evidence base for the treatment of such patients in clinical practice. Sponsors and investigators should consider careful modification of the enrollment criteria to improve the inclusion of older individuals who make up the major proportion of cancer patients population.
Treatment with β-blocker nebivolol ameliorates oxidative stress and endothelial dysfunction in tenofovir-induced nephrotoxicity in rats
Authors: Nascimento Mariana Moura , Bernardo Desiree Rita Denelle , de Bragança Ana Carolina , Massola Shimizu Maria Heloisa , Seguro Antonio Carlos , Volpini Rildo Aparecido , Canale Daniele
Published: August 2022

Background

Tenofovir disoproxil fumarate (TDF), a widely prescribed component in antiretroviral regimens, has been associated with nephrotoxicity. Nebivolol is a third generation selective β-1 adrenergic receptor blocker and may protect renal structure and function through the suppression of oxidative stress and enhancement of nitric oxide (NO) synthesis. We aimed to investigate whether nebivolol could be an effective therapeutic strategy to mitigate tenofovir-induced nephrotoxicity.

Methods

We allocated Wistar rats to four groups: control (C), received a standard diet for 30 days; NBV, received a standard diet for 30 days added with nebivolol (100 mg/kg food) in the last 15 days; TDF, received a standard diet added with tenofovir (300 mg/kg food) for 30 days; and TDF+NBV, received a standard diet added with tenofovir for 30 days and nebivolol in the last 15 days.

Results

Long-term exposure to tenofovir led to impaired renal function, induced hypertension, endothelial dysfunction and oxidative stress. Nebivolol treatment partially recovered glomerular filtration rate, improved renal injury, normalized blood pressure and attenuated renal vasoconstriction. Administration of nebivolol contributed to reductions in asymmetric dimethylarginine (ADMA) levels as well as increases in endothelial nitric oxide sintase (eNOS) accompanied by renin-angiotensin-aldosterone system downregulation and decreases in macrophage and T-cells infiltrate. Furthermore, nebivolol was responsible for the maintenance of the adequate balance of thiobarbituric acid reactive substances (TBARS) and glutathione (GSH) levels and it was associated with reductions in NADPH oxidase (NOX) subunits.

Conclusion

Nebivolol holds multifaceted actions that promote an advantageous option to slow the progression of kidney injury in tenofovir-induced nephrotoxicity.
Volatile organic compound profiling as a potential biomarker in irritable bowel syndrome: A feasibility study
Authors: Van Malderen Kathleen , Hanning Nikita , Lambrechts Helen , Haverhals Tine , Van Marcke Silke , Ceuleers Hannah , De Man Joris G. , De Winter Benedicte Y. , Lamote Kevin , De Schepper Heiko U.
Published: August 2022

Background

Irritable bowel syndrome (IBS) is a chronic gastrointestinal disorder for which no diagnostic tools are currently available. Patients are diagnosed using the Rome IV criteria and subtyped into a diarrhea, constipation, or mixed phenotype based on their dominant stool pattern. A recent development in the biomarker area is the analysis of volatile organic compounds (VOCs). The aim of this study was to evaluate the potential of VOCs as diagnostic and phenotypic biomarkers for IBS in breath and fecal samples.

Materials and methods

Breath and fecal samples from IBS patients and healthy asymptomatic controls (HC) were analyzed with multicapillary column/ion mobility spectrometry (MCC/IMS) and classification models were created based upon VOCs and clinical characteristics.

Discussion

Irritable bowel syndrome patients were differentiated from HC by means of volatile profiling in both breath and fecal samples with area under the curve (AUCs) of respectively 0.62 and 0.80. Patient subtypes could also be differentiated from each other with AUCs ranging between 0.65 and 0.78. Furthermore, VOC models could differentiate IBS patients based on clinical characteristics like psychological comorbidities and microbiota-influencing therapies.

Conclusion

This study is the first to demonstrate the use of VOC profiling with the help of MCC/IMS to differentiate IBS patients. Furthermore, the importance of clinical characteristics beside the dominant stool pattern in the differentiation of IBS patients was emphasized.
Case report: Thoracic and lumbar plasma cell myeloma mimicking hemangiomas on MRI and 18F-FDG PET/CT
Authors: Hu Xianwen , Xiong Wei , Li Shun , Li Xue , Cai Jiong , Wang Pan , Li Dandan
Published: August 2022

Plasma cell myeloma (PCM) is a malignant clonal disease of abnormal proliferation of plasma cells, which is the second most common hematological malignancy after leukemia. PCM often diffuses and involves the bones of the whole body, especially the spinal column, ribs, skull, pelvis, and other axial bones and flat bones. Herein, we present a 55-year-old man who came to the hospital seeking medical help for low-back pain and numbness in his lower limbs. Computed tomography (CT) was performed because the clinician suspected that the patient had a herniated disc, and the results showed that the 7th thoracic vertebrae and the 3rd lumbar vertebrae showed a low density of bone destruction with “honeycombing” changes. Magnetic resonance imaging (MRI) showed that the corresponding lesions presented long T1 and long T2 signals, and the lesions were significantly enhanced in contrast-enhanced T1WI sequences, and fluoro18-labeled deoxyglucose positron emission tomography/computed tomography (18F-FDG PET/CT) showed mild radioactive uptake in the lesions. Based on these imaging findings, the patient was considered for a diagnosis of hemangiomas, and surgery was performed because the affected vertebra was pressing on the spinal cord. However, intraoperative frozen section examination showed that the patient had plasma cell myeloma. Our case study suggests that PCM involving a single thoracic and lumbar spine is rare and should be considered as one of the imaging differential diagnoses of hemangiomas. Moreover, the diagnosis of PCM is difficult when the number of lesions is small, especially when the plasma cell ratio is within the normal reference range in laboratory tests.
The diversity in antimicrobial resistance of MDR Enterobacteriaceae among Chinese broiler and laying farms and two mcr-1 positive plasmids revealed their resistance-transmission risk
Authors: Zong Shuaizhou , Xu Dingting , Zheng Xiner , Zaeim Davood , Wang Peng , Han Jianzhong , Qu Daofeng
Published: August 2022

This research aimed to investigate the microbial composition and diversity of antimicrobial resistance genes (ARGs) found in Chinese broiler and layer family poultry farms. We focused on the differences in resistance phenotypes and genotypes of multidrug-resistant Enterobacteriaceae (MDRE) isolated from the two farming environments and the existence and transmissibility of colistin resistance gene mcr-1. Metagenomic analysis showed that Firmicutes and Bacteroides were the dominant bacteria in broiler and layer farms. Many aminoglycoside and tetracycline resistance genes were accumulated in these environments, and their absolute abundance was higher in broiler than in layer farms. A total of 526 MDRE were isolated with a similar distribution in both farms. The results of the K-B test showed that the resistance rate to seven antimicrobials including polymyxin B and meropenem in broiler poultry farms was significantly higher than that in layer poultry farms (P ≤ 0.05). PCR screening results revealed that the detection rates of mcr-1, aph(3’)Ia, aadA2, blaoxa–1, blaCTX–M, fosB, qnrD, sul1, tetA, and catA1 in broiler source MDRE were significantly higher than those in layers (P ≤0.05). A chimeric plasmid p20432-mcr which carried the novel integron In1866 was isolated from broiler source MDRE. The high frequency of conjugation (10–1 to 10–3) and a wide range of hosts made p20432-mcr likely to play an essential role in the high detection rate of mcr-1, aph(3’)-Ia, and aadA2 in broiler farms. These findings will help optimize disinfection and improve antimicrobial-resistant bacteria surveillance programs in poultry farms, especially broilers.
Oligotrophy vs. copiotrophy in an alkaline and saline habitat of Lonar Lake
Authors: Nimonkar Yogesh S. , Godambe Tejashree , Kulkarni Apurva , Patel Tarachand , Paul Dhreej , Paul Debarati , Rale Vinay , Prakash Om
Published: August 2022

We reported our comparative observations on oligotrophs vs. copiotrophs from a hyper-alkaline and hypersaline habitat, Lonar Lake, situated in the Buldhana district of Maharashtra, India. Cell numbers of oligotrophic and copiotrophic microbes from the sediment were enumerated by the three-tube most probable number (MPN) method using an array of nutrient-rich and oligotrophic (≈10–20 mg carbon L−1) media offering simulated natural conditions of pH and salinity. A total of 50 strains from 15 different genera and 30 different species were isolated from the highest positive dilutions of MPN to identify the taxa of oligotrophs and copiotrophic microorganisms dominating in Lonar Lake. We did not get any true oligotrophs due to their adaptation to higher carbon levels during the isolation procedure. On the contrary, several true copiotrophs, which could not adapt and survive on a low-carbon medium, were isolated. It is also observed that changes in medium composition and nutrient level altered the selection of organisms from the same sample. Our data indicate that copiotrophic microorganisms dominate the eutrophic Lonar Lake, which is also supported by the past metagenomics studies from the same site. We also reported that quick depletion of carbon from oligotrophic medium worked as a limiting factor, inducing cell death after 2–3 generations and preventing the development of visible colonies on plates and sufficient optical density in liquid medium. Therefore, a long-term supply of low levels of carbon, followed by isolation on enriched media, can serve as a good strategy in isolation of novel taxa of microorganism, with industrial or environmental importance.
Locally generated C3 regulates the clearance of Toxoplasma gondii by IFN-γ-primed macrophage through regulation of xenophagy
Authors: Liu Bo , Yan Yan , Wang Xiaoreng , Chen Nannan , Wu Jue
Published: August 2022

Exogenous pathogen infection can induce autophagy in cells. Autophagy is essential for cell survival, development, and homeostasis. It not only regulates cell defense and stress, but also has a close relationship with innate and adaptive immunity. Complement is an important part of innate immunity, which could be activated by three approaches, including classic, alternative, and lectin pathways. All the three pathways result in the activation of C3, and generate anaphylatoxin fragments C3a and C5a, and formation of the membrane attack complex. Either C3a or C5a induces the inflammatory cytokines through binding to C3aR or C5aR, respectively. However, it is still unknown whether the complement could regulate the autophagy of intracellular microorganisms or not. In this study, we constructed a Toxoplasma gondii (T. gondii) and macrophages co-culture experimental model using T. gondii expressing enhanced green fluorescence protein (EGFP) fluorescence and C3−/-C57BL/6 J mice for that T. gondii invaded peritoneal macrophages in mice. Western blot, laser confocal microscopy (LCM), and transmission electron microscopy (TEM) were used to observe the changes of autophagy between the macrophages from wild-type (WT) and C3−/− mice. Flow cytometry and LCM were used to investigate the effect of autophagy on the killing ability of macrophages against T. gondii. Here, we found that local C3 could suppress not only the canonical autophagy of macrophage, but also the xenophagy to T. gondii. Interestingly, the inhibition of C3 on host cell autophagy could significantly suppress the clearance of T. gondii by the IFN-γ-primed macrophage. Finally, we investigated the mechanism of the autophagy regulation of C3 that the effect of C3 on the macrophage-specific autophagy against T. gondii depends on mTOR. And, there is C3a but not C5a/C5aR involved in regulating macrophage xenophagy against T. gondii. Collectively, our findings suggest locally generated C3 regulates the clearance of T. gondii by Macrophage through the regulation of the non-canonical IFN-γ-dependent autophagy pathway, and paint a clearer picture in the regulation of autophagy by innate immune components.
Genome analysis of the candidate phylum MBNT15 bacterium from a boreal peatland predicted its respiratory versatility and dissimilatory iron metabolism
Authors: Begmatov Shahjahon , Beletsky Alexey V. , Dedysh Svetlana N. , Mardanov Andrey V. , Ravin Nikolai V.
Published: August 2022

Uncultured bacteria of the candidate phylum MBNT15, distantly related to Desulfobacterota, have been identified in a broad range of mostly organic-rich aquatic environments. We assembled a near-complete genome of a member of MBNT15 from a boreal peatland metagenome and used genomic data to analyze the metabolic pathways of this bacterium and its ecological role. This bacterium, designated SHF-111, was predicted to be rod shaped, it lacks flagellar machinery but twitching motility is encoded. Genome-based phylogenetic analysis supported the phylum-level classification of the MBNT15 lineage. Genome annotation and metabolic reconstruction revealed the presence of the Embden–Meyerhof, Entner–Doudoroff and pentose phosphate pathways, as well as the complete tricarboxylic acid (TCA) cycle, and suggested a facultatively anaerobic chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, fatty acids and simple sugars, and completely oxidize these substrates through aerobic and anaerobic respiration. The SHF-111 genome encodes multiple multiheme c-type cytochromes that probably enable dissimilatory iron reduction. Consistently, the relative abundance of MBNT15 in peatlands positively correlated with iron concentration. Apparently, in the wetland ecosystem, MBNT15 representatives play the role of scavengers, carrying out the complete mineralization of low molecular weight organic substances formed as a result of microbial degradation of complex polymeric substrates. Comparative genome analysis of the MBNT15 phylum revealed that vast majority of its members are capable of aerobic respiration and dissimilatory iron reduction and some species also can reduce sulfur and nitrogen compounds, but not sulfate. Based on phylogenetic and genomic analyses, the novel bacterium is proposed to be classified as Candidatus Deferrimicrobium borealis, within a candidate phylum Deferrimicrobiota.
Transcriptome and metabolome analyses reveal transcription factors regulating ganoderic acid biosynthesis in Ganoderma lucidum development
Authors: Meng Li , Zhou Ruyue , Lin Jialong , Zang Xizhe , Wang Qingji , Wang Panmeng , Wang Li , Li Zhuang , Wang Wei
Published: August 2022

Ganoderma lucidum is an important medicinal fungus in Asian countries. Ganoderic acid (GA) is the major variety of bioactive and medicative components in G. lucidum. Biosynthesis of secondary metabolites is usually associated with cell differentiation and development. However, the mechanism underlying these phenomena remain unclear. Transcription factors play an essential regulatory role in the signal transduction pathway, owing to the fact that they represent the major link between signal transduction and expression of target genes. In the present study, we performed transcriptome and metabolome analyses to identify transcription factors involved in GA biosynthesis during development of G. lucidum. Transcriptome data revealed differentially expressed genes between mycelia and primordia, as well as between mycelia and the fruiting body. Results from gene ontology enrichment analysis and metabolome analyses suggested that GAs and flavonoids biosynthetic process significantly changed during fungal development. The analysis of predicted occurrences of DNA-binding domains revealed a set of 53 potential transcription factor families in G. lucidum. Notably, we found homeobox transcription factor and velvet family protein played important role in GA biosynthesis. Combined with previous studies, we provided a model diagram of transcription factors involved in GA biosynthesis during fruiting body formation. Collectively, these results are expected to enhance our understanding into the mechanisms underlying secondary metabolite biosynthesis and development in fungi.
Proteome profiling of evolved methicillin-resistant Staphylococcus aureus strains with distinct daptomycin tolerance and resistance phenotypes
Authors: Sulaiman Jordy Evan , Long Lexin , Qian Pei-Yuan , Lam Henry
Published: August 2022

Methicillin-resistant Staphylococcus aureus (MRSA) is a highly dangerous pathogen, and daptomycin has been increasingly used to treat its infections in clinics. Recently, several groups have shown that tolerance and resistance of microbes can evolve rapidly under cyclic antibiotic exposure. We have previously shown that the same tolerance and resistance development occurs in MRSA treated with daptomycin in an adaptive laboratory evolution (ALE) experiment. In the present study, we performed proteomic analysis to compare six daptomycin-tolerant and resistant MRSA strains that were evolved from the same ancestral strain. The strain with a higher tolerance level than the others had the most different proteome and response to antibiotic treatment, resembling those observed in persister cells, which are small subpopulations of bacteria that survive lethal antibiotics treatment. By comparing the proteome changes across strains with similar phenotypes, we identified the key proteins that play important roles in daptomycin tolerance and resistance in MRSA. We selected two candidates to be confirmed by gene overexpression analysis. Overexpression of EcsA1 and FabG, which were up-regulated in all of the tolerant evolved strains, led to increased daptomycin tolerance in wild-type MRSA. The proteomics data also suggested that cell wall modulations were implicated in both resistance and tolerance, but in different ways. While the resistant strains had peptidoglycan changes and a more positive surface charge to directly repel daptomycin, the tolerant strains possessed different cell wall changes that do not involve the peptidoglycan nor alterations of the surface charge. Overall, our study showed the differential proteome profiles among multiple tolerant and resistant strains, pinpointed the key proteins for the two phenotypes and revealed the differences in cell wall modulations between the daptomycin-tolerant/resistant strains.
Anomaly detection as vision-based obstacle detection for vehicle automation in industrial environment
Authors: Wenning Marius , Adlon Tobias , Burggräf Peter
Published: August 2022

Nowadays, produced cars are equipped with mechatronical actuators as well as with a wide range of sensors in order to realize driver assistance functions. These components could enable cars’ automation at low speeds on company premises, although autonomous driving in public traffic is still facing technical and legal challenges. For automating vehicles in an industrial environment a reliable obstacle detection system is required. State-of-the-art solution for protective devices in Automated Guided Vehicles is the distance measuring laser scanner. Since laser scanners are not basic equipment of today’s cars in contrast to monocameras mounted behind the windscreen, we develop a computer vision algorithm that is able to detect obstacles in camera images reliably. Therefore, we make use of our well-known operational design domain by teaching an anomaly detection how the vehicle path should look like. The result is an anomaly detection algorithm that consists of a pre-trained feature extractor and a shallow classifier, modelling the probability of occurrence. We record a data set of a real industrial environment and show a robust classifier after training the algorithm with images of only one run. The performance as an obstacle detection is on par with a semantic segmentation, but requires a fraction of the training data and no labeling.
Rodent models of early adversity: Impacts on developing social behavior circuitry and clinical implications
Authors: Packard Katherine , Opendak Maya
Published: August 2022

Flexible and context-appropriate social functioning is key for survival across species. This flexibility also renders social behavior highly plastic, particularly during early development when attachment to caregiver can provide a template for future social processing. As a result, early caregiving adversity can have unique and lasting impacts on social behavior and even confer vulnerability to psychiatric disorders. However, the neural circuit mechanisms translating experience to outcome remain poorly understood. Here, we consider social behavior scaffolding through the lens of reward and threat processing. We begin by surveying several complementary rodent models of early adversity, which together have highlighted impacts on neural circuits processing social cues. We next explore these circuits underlying perturbed social functioning with focus on dopamine (DA) and its role in regions implicated in social and threat processing such as the prefrontal cortex (PFC), basolateral amygdala (BLA) and the lateral habenula (LHb). Finally, we turn to human populations once more to examine how altered DA signaling and LHb dysfunction may play a role in social anhedonia, a common feature in diagnoses such as schizophrenia and major depressive disorder (MDD). We argue that this translational focus is critical for identifying specific features of adversity that confer heightened vulnerability for clinical outcomes involving social cue processing.
Conditioned stimulus effects on paired or alternative reinforcement depend on presentation duration: Implications for conceptualizations of craving
Authors: Ginsburg Brett C. , Nawrocik-Madrid Acacia , Schindler Charles W. , Lamb R. J.
Published: August 2022

Conditioned stimuli (CS) associated with alcohol ingestion are thought to play a role in relapse by producing a craving that in turn increases motivation to drink which increases ethanol-seeking and disrupts other ongoing behavior. Alternatively, such CS may provide information indicating a likely increase in the density of the paired unconditioned stimulus and simultaneously elicit behavior that may be incompatible with other ongoing behavior, i.e., approach toward the CS. To explore these possibilities, rats were trained to respond for ethanol or food in two different components of the same session after which a light above the ethanol-lever was lighted twice during each component and each light presentation was followed by ethanol delivery. The duration of this CS was 10 s initially and then increased to 30 s, then to 100 s, and finally returned to 30 s. The change in responding for ethanol or food was compared to a matched period immediately preceding CS presentation. The CS presentation increased responding to ethanol, and this effectincreaseswith longer CS presentations. In contrast, the CS presentation decreased responding to food, and this effectdecreaseswith longer CS presentations. These results appear to support the informational account of CS action rather than simply a change in the motivation to seek and consume ethanol. This suggests that craving as it is commonly understood likely represents multiple behavioral processes, not simply increased desire for alcohol and that reports of craving likely reflect labeling based upon past experiences rather than a cause of future drug-taking.
Recognition of musical beat and style and applications in interactive humanoid robot
Authors: Chu Yue
Published: August 2022

The musical beat and style recognition have high application value in music information retrieval. However, the traditional methods mostly use a convolutional neural network (CNN) as the backbone and have poor performance. Accordingly, the present work chooses a recurrent neural network (RNN) in deep learning (DL) to identify musical beats and styles. The proposed model is applied to an interactive humanoid robot. First, DL-based musical beat and style recognition technologies are studied. On this basis, a note beat recognition method combining attention mechanism (AM) and independent RNN (IndRNN) [AM-IndRNN] is proposed. The AM-IndRNN can effectively avoid gradient vanishing and gradient exploding. Second, the audio music files are divided into multiple styles using the music signal's temporal features. A human dancing robot using a multimodal drive is constructed. Finally, the proposed method is tested. The results show that the proposed AM-IndRNN outperforms multiple parallel long short-term memory (LSTM) models and IndRNN in recognition accuracy (88.9%) and loss rate (0.0748). Therefore, the AM-optimized LSTM model has gained a higher recognition accuracy. The research results provide specific ideas for applying DL technology in musical beat and style recognition.
Regulation of N6-methyladenosine (m6A) RNA methylation in microglia-mediated inflammation and ischemic stroke
Authors: Zhang Fangfang , Ran Yuanyuan , Tahir Muhammad , Li Zihan , Wang Jianan , Chen Xuechai
Published: August 2022

N6-methyladenosine (m6A) is the most abundant post-transcription modification, widely occurring in eukaryotic mRNA and non-coding RNA. m6A modification is highly enriched in the mammalian brain and is associated with neurological diseases like Alzheimer’s disease (AD) and Parkinson’s disease (PD). Ischemic stroke (IS) was discovered to alter the cerebral m6A epi-transcriptome, which might have functional implications in post-stroke pathophysiology. Moreover, it is observed that m6A modification could regulate microglia’s pro-inflammatory and anti-inflammatory responses. Given the critical regulatory role of microglia in the inflammatory processes in the central nervous system (CNS), we speculate that m6A modification could modulate the post-stroke microglial inflammatory responses. This review summarizes the vital regulatory roles of m6A modification in microglia-mediated inflammation and IS. Stroke is associated with a high recurrence rate, understanding the relationship between m6A modification and stroke may help stroke rehabilitation and develop novel therapies in the future.
Attachment style dimensions are associated with neural activation during projection of mental states
Authors: Lai Carlo , Ciacchella Chiara , Altavilla Daniela , Veneziani Giorgio , Aceto Paola , Cecchini Marco , Luciani Massimiliano
Published: August 2022

The aim of the present study was to investigate the association between attachment dimensions and neural correlates in response to the Rorschach inkblots. Twenty-seven healthy volunteers were recruited for the electroencephalographic registration during a visual presentation of the Rorschach inkblots and polygonal shapes. The Attachment Style Questionnaire (ASQ) was administered to participants. Correlations between the ASQ scores and standardized low-resolution brain electromagnetic tomography (sLORETA) intensities were performed. The Rorschach inkblots elicited several projective responses greater than the polygonal shapes (distortions, human and total movements, and embellishments). Only during the Rorschach inkblots presentation, discomfort with closeness and relationships as secondary subscales were negatively correlated with the activation of right hippocampus, parahippocampus, amygdala, and insula; need for approval subscale was negatively correlated with the activation of orbital and prefrontal cortex and left hippocampus. Moreover, the correlations between attachment dimensions and neural activation during the Rorschach inkblots were significantly higher compared to the same correlations in response to polygonal shapes. These findings suggest that attachment style can modulate brain activation during the projective activity of the Rorschach inkblots.
A mini-review of the role of condensin in human nervous system diseases
Authors: Pang Du , Yu Shengping , Yang Xuejun
Published: August 2022

Mitosis and meiosis are crucial life activities that transmit eukaryotic genetic information to progeny in a stable and orderly manner. The formation and appearance of chromosomes, which are derived from chromatin, are the preconditions and signs of mitosis. When entering mitosis, interphase loose chromatin is highly spiralized and folded to form compact chromosomes. In recent years, it has been found that in addition to the well-known DNA, histones, and topoisomerase, a large protein complex called condensin plays an important role in the process of chromosome formation. Numerous studies have shown that the abnormal function of condensin can lead to incomplete or excessive concentration of chromatin, as well as disorder of genome organization process, abnormal transmission of genetic information, and ultimately lead to various diseases of individual, especially in nervous system diseases. In this review, the biological function of condensin and the potential pathogenic mechanism of condensin in nervous system diseases are briefly summarized. Therefore, the investigation of these mechanisms makes a significant contribution to the understanding of those related diseases and provides new ideas for clinical treatments.
The effects of Crocus sativus L. (Saffron) and its ingredients on dietary intakes in cardiovascular disease in Iranian population: A systematic review and meta-analysis
Authors: Kianmehr Majid , Mahdizadeh Fateme , Khazdair Mohammad Reza
Published: August 2022

Cardiovascular disease (CVD) is one of the most common causes of mortality around the world. The aim of this study is to summarize and conclude the clinical evidence regarding the use of Crocus sativus (C. sativus) and its ingredients on cardiovascular risk factors. A systematic search was conducted with PubMed, Web of Science (ISI), and Scopus in the English language from 2015 until September 2021. A fixed-effect or random-effects model were applied to pool standard mean difference (SMD) and its 95 % confidence intervals (CI). Randomized controlled studies that assessed the clinical effects of C. sativus and its ingredients on dietary intake (Energy, Carbohydrate, Protein, and total Fat) in human subjects were included. Seven studies comprising 421 participants were included in the meta-analysis. Pooling of results showed significant effect of saffron on total fat (−0.14; 95% CI: −0.49 to 0.20; I2 = 57.3%) and significant effect of crocin on Energy (0.94; 95% CI: −0.77 to 2.65; I2 = 95.9%), Carbohydrate (0.44; 95% CI: −0.74 to 1.62; I2 = 92.6%), and Protein (−0.04; 95% CI: −0.26 to 0.34; I2 = 0.0%). Present meta-analysis suggests that treatment with crocins is more effective than saffron in energy, carbohydrate, and protein, while saffron is more effective than crocins in fat. However, further studies are needed to confirm these findings.
A Nutrition-Related Factor-Based Risk Stratification for Exploring the Clinical Benefits in the Treatment of Patients With Locally Advanced Esophageal Squamous Cell Carcinoma Receiving Definitive Chemoradiotherapy: A Retrospective Cohort Study
Authors: Yu Yilin , Wu Haishan , Qiu Jianjian , Ke Dongmei , Wu Yahua , Lin Mingqiang , Liu Tianxiu , Zheng Qunhao , Zheng Hongying , Yang Jun , Wang Zhiping , Li Hui , Liu Lingyun , Yao Qiwei , Li Jiancheng , Cheng Wenfang , Chen Xiaohui
Published: August 2022

Objective

No study has reported the risk stratification of BMI and PNI in patients with locally advanced esophageal squamous cell carcinoma (ESCC) undergoing definitive chemoradiotherapy (dCRT). This study aimed to construct a risk stratification to guide the treatment of ESCC following dCRT.

Methods

A total of 1,068 patients with locally advanced ESCC who received dCRT were retrospectively analyzed. The impacts of clinicopathological factors on overall survival (OS) and progression-free survival (PFS) were analyzed. Besides, the novel prognostic indices of pre-therapeutic nutritional index (PTNI) and prognostic index (PI) were developed.

Results

The median follow-up period of OS and PFS were 22.9 and 17.4 months, respectively. The high body mass index (BMI) group had better 5-year OS and PFS (36.4 and 34.0%) than the low BMI group (18.8 and 17.2%). The high prognostic nutritional index (PNI) group also had better 5-year OS and PFS (33.4 and 30.9%) than the low PNI group (17.5 and 17.2%). Multivariate Cox regression analysis showed that BMI and PNI were independent prognostic factors for OS and PFS. Based on nutritional indices, patients were categorized into the low-risk (PTNI = 1), medium-risk (PTNI = 2), and high-risk (PTNI = 3) groups with 5-year OS rates of 38.5, 18.9, 17.5%, respectively (p < 0.001) and 5-year PFS rates of 35.8, 17.6, 16.8%, respectively (p < 0.001). Besides, we also constructed a prognostic index (PI) for OS and PFS which was calculated based on statistically significant factors for predicting OS and PFS. The results revealed that the high-risk group had worse OS and PFS than the low-risk group (p < 0.001). Finally, RCS analysis demonstrated a non-linear relationship between the PNI, BMI, and survival for patients with ESCC. The death hazard of PNI and BMI sharply decreased to 41.8 and 19.7.

Conclusion

The decreased pre-therapeutic BMI and PNI levels were associated with a worse survival outcome. BMI and PNI are readily available and can be used to stratify risk factors for locally advanced ESCC patients undergoing dCRT. The novel risk stratification may help to evaluate patients’ pre-therapeutic status and guide dCRT for locally advanced ESCC patients.