bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantifying the roles of food intake and stored lipid for growth and development throughout the life cycle of a high-latitude copepod, and consequences for ocean carbon sequestration
Authors: Anderson Thomas R. , Hessen Dag O. , Gentleman Wendy C. , Yool Andrew , Mayor Daniel J.
Published: July 2022

Copepods are a critical component of ocean ecosystems, providing an important link between phytoplankton and higher trophic levels as well as regulating biogeochemical cycles of carbon (C) and nutrients. Lipid-rich animals overwinter in deep waters where their respiration may sequester a similar quantity of C as that due to sinking detritus. This ‘seasonal lipid pump’ nevertheless remains absent from global biogeochemical models that are used to project future ocean-climate interactions. Here, we make an important step to resolving this omission by investigating the biogeochemical cycling of C and nitrogen (N) by high-latitude copepods using a new individual-based stoichiometric model that includes explicit representation of lipid reserves. Simulations are presented for Calanus finmarchicus throughout its life cycle at Station Mike (66°N, 2°E) in the Norwegian Sea, although the model is applicable to any suitable location and species with a similar life history. Results indicate that growth, development and egg production in surface waters are driven primarily by food intake (quantity) which provides a good stoichiometric match to metabolic requirements. In contrast, the main function of stored lipid is to support overwintering respiration and gonad development with these two processes respectively accounting for 19 and 55% of the lipid accumulated during the previous spring/summer. The animals also catabolise 41% of body protein in order to provide N for the maintenance of structural biomass. In total, each individual copepod sequesters 9.6 μmol C in deep water. If the areal density of animals is 15,000–40,000 m-2, these losses correspond to a sequestration of 1.7–4.6 g C m-2 yr-1. Lipids contribute only 1% of the C used in egg production in the following year. Accumulating extra lipid in spring would potentially increase egg production but our analysis suggests that any such benefit is outweighed by a higher risk of predator mortality. Our work indicates that the seasonal lipid pump may be of similar magnitude to C sequestration via sinking particles in the North Atlantic and highlights the need for improved physiological understanding of lipid use by high-latitude copepods in order to better constrain C fluxes in ocean food-webs and biogeochemical models.
Diver-generated photomosaics as a tool for monitoring temperate rocky reef ecosystems
Authors: Spyksma Arie J. P. , Miller Kelsey I. , Shears Nick T.
Published: July 2022

Robust monitoring data provides important information on ecosystem responses to anthropogenic stressors; however, traditional monitoring methodologies, which rely heavily on time in the field, are resource intensive. Consequently, trade-offs between data metrics captured and overall spatial and temporal coverage are necessary to fit within realistic monitoring budgets and timeframes. Recent advances in remote sensing technology have reduced the severity of these trade-offs by providing cost-effective, high-quality data at greatly increased temporal and spatial scales. Structure-from-motion (SfM) photogrammetry, a form of remote sensing utilising numerous overlapping images, is well established in terrestrial applications and can be a key tool for monitoring changes in marine benthic ecosystems, which are particularly vulnerable to anthropogenic stressors. Diver-generated photomosaics, an output of SfM photogrammetry, are increasingly being used as a benthic monitoring tool in clear tropical waters, but their utility within temperate rocky reef ecosystems has received less attention. Here we compared benthic monitoring data collected from virtual quadrats placed on photomosaics with traditional diver-based field quadrats to understand the strengths and weaknesses of using photomosaics for monitoring temperate rocky reef ecosystems. In north-eastern New Zealand, we evaluated these methods at three sites where sea urchin barrens were prevalent. We found key metrics (sea urchin densities, macroalgae canopy cover and benthic community cover) were similar between the two methods, but data collected via photogrammetry were quicker, requiring significantly less field time and resources, and allowed greater spatial coverage than diver-based field quadrats. However, the use of photomosaics was limited by high macroalgal canopy cover, shallow water and rough sea state which reduced stitching success and obscured substratum and understory species. The results demonstrate that photomosaics can be used as a resource efficient and robust method for effectively assessing and monitoring key metrics on temperate rocky reef ecosystems.
On the adhesion between thin sheets and randomly rough surfaces
Authors: Wang Anle , Müser Martin H.
Published: July 2022

Thin, elastic sheets are well known to adapt to rough counterfaces, whereby adhesive interactions and pull-off stresses σp can be significant, yet no generally applicable, quantitative guideline has been suggested hitherto as to when a sheet should be considered thin enough to be sticky. Using computer simulations, we find that the dependence of σp on surface energy γ has a high and a low-pull-off-stress regime. For randomly rough surfaces, we locate the dividing line at the point, where γ is approximately half the elastic energy per unit area needed to make conformal contact, which is the same ratio as for semi-infinite elastic solids. This rule of thumb also applies to a certain degree for single-wavelength roughness, in which case the transition from low to high stickiness occurs when at the moment of maximum tension contact is not only broken at the height maxima but also at the saddle points.
An Umbrella Review With Meta-Analysis of Chest Computed Tomography for Diagnosis of COVID-19: Considerations for Trauma Patient Management
Authors: Gempeler Andrés , Griswold Dylan P. , Rosseau Gail , Johnson Walter D. , Kaseje Neema , Kolias Angelos , Hutchinson Peter J. , Rubiano Andres M.
Published: July 2022

Background

RT-PCR testing is the standard for diagnosis of COVID-19, although it has its suboptimal sensitivity. Chest computed tomography (CT) has been proposed as an additional tool with diagnostic value, and several reports from primary and secondary studies that assessed its diagnostic accuracy are already available. To inform recommendations and practice regarding the use of chest CT in the in the trauma setting, we sought to identify, appraise, and summarize the available evidence on the diagnostic accuracy of chest CT for diagnosis of COVID-19, and its application in emergency trauma surgery patients; overcoming limitations of previous reports regarding chest CT accuracy and discussing important considerations regarding its role in this setting.

Methods

We conducted an umbrella review using Living Overview of Evidence platform for COVID-19, which performs regular automated searches in MEDLINE, Embase, Cochrane Central Register of Controlled Trials, and more than 30 other sources. The review was conducted following the JBI methodology for systematic reviews. The Grading of Recommendations, Assessment, Development, and Evaluation approach for grading the certainty of the evidence is reported (registered in International Prospective Register of Systematic Reviews, CRD42020198267).

Results

Thirty studies that fulfilled selection criteria were included; 19 primary studies provided estimates of sensitivity (0.91, 95%CI = [0.88–0.93]) and specificity (0.73, 95%CI = [0.61; 0.82]) of chest CT for COVID-19. No correlation was found between sensitivities and specificities (ρ = 0.22, IC95% [–0.33; 0.66]). Diagnostic odds ratio was estimated at: DOR = 27.5, 95%CI (14.7; 48.5). Evidence for sensitivity estimates was graded as MODERATE, and for specificity estimates it was graded as LOW.

Conclusion

The value of chest CT appears to be that of an additional screening tool that can easily detect PCR false negatives, which are reportedly highly frequent. Upon the absence of PCR testing and impossibility to perform RT-PCR in trauma patients, chest CT can serve as a substitute with increased value and easy implementation.

Systematic Review Registration

[www.crd.york.ac.uk/prospero], identifier [CRD42020198267].
Effectiveness of a lifestyle modification programme in the treatment of depression symptoms in primary care
Authors: Aguilar-Latorre Alejandra , Pérez Algorta Guillermo , Navarro-Guzmán Capilla , Serrano-Ripoll María J. , Oliván-Blázquez Bárbara
Published: July 2022

Background

Depression symptoms are prevalent in the general population, and their onset and continuation may be related to biological and psychosocial factors, many of which are related to lifestyle aspects. Health promotion and lifestyle modification programmes (LMPs) may be effective on reducing the symptoms. The objective of this study was to analyse the clinical effectiveness of a LMP and a LMP plus Information and Communication Technologies, when compared to Treatment as Usual (TAU) over 6 months. The interventions were offered as an adjuvant treatment delivered in Primary Healthcare Centers (PHCs) for people with depression symptoms.

Methods

We conducted an open-label, multicentre, pragmatic, randomized clinical trial. Participants were recruited from several PHCs. Those participants visiting general practitioner for any reason, who also met the inclusion criteria (scoring 10 to 30 points on the Beck II Self-Applied Depression Inventory) were invited to take part in the study. TAU+LMP consisted of six weekly 90-min group sessions focused on improving lifestyle. TAU+LMP + ICTs replicated the TAU+LMP format, plus the addition of a wearable smartwatch to measure daily minutes walked and sleep patterns. A total of 188 participants consented to participate in the study and were randomized. We used linear mixed models, with a random intercept and an unstructured covariance to evaluate the impact of the interventions compared to TAU.

Results

Both interventions showed a statistically significant reduction on depressive symptoms compared to TAU (TAU+LMP vs. TAU slope difference, b = −3.38, 95% CI= [−5.286, −1.474] p = 0.001 and TAU+LMP+ICTs vs. TAU slope difference, b = −4.05, 95% CI = [−5.919, −2.197], p < 0.001). These reductions imply a moderate effect size. In the TAU+LMP+ICTs there was a significant increase regarding minutes walking per week (b = 99.77) and adherence to Mediterranean diet (b = 0.702). In the TAU+LMP there was a significant decrease regarding bad sleep quality (b = −1.24).

Conclusion

TAU+LMPs administered in PHCs to people experiencing depression symptoms were effective on reducing these symptoms compared to TAU. They also have a positive impact on changing several lifestyle factors. These findings indicate that these interventions can be promising strategies for PHCs.
Molecular characterization of florfenicol and oxazolidinone resistance in Enterococcus isolates from animals in China
Authors: Li Pingping , Gao Mengdi , Feng Chunlin , Yan Tielun , Sheng Zhiqiong , Shi Weina , Liu Shuang , Zhang Lei , Li Anqi , Lu Junwan , Lin Xi , Li Kewei , Xu Teng , Bao Qiyu , Sun Caixia
Published: July 2022

Florfenicol is widely used for the treatment of bacterial infections in domestic animals. The aim of this study was to analyze the molecular mechanisms of florfenicol and oxazolidinone resistance in Enterococcus isolates from anal feces of domestic animals. The minimum inhibitory concentration (MIC) levels were determined by the agar dilution method. Polymerase chain reaction (PCR) was performed to analyze the distribution of the resistance genes. Whole-genome sequencing and comparative plasmid analysis was conducted to analyze the resistance gene environment. A total of 351 non-duplicated enteric strains were obtained. Among these isolates, 22 Enterococcus isolates, including 19 Enterococcus. faecium and 3 Enterococcus. faecalis, were further studied. 31 florfenicol resistance genes (13 fexA, 3 fexB, 12 optrA, and 3 poxtA genes) were identified in 15 of the 19 E. faecium isolates, and no florfenicol or oxazolidinone resistance genes were identified in 3 E. faecalis isolates. Whole-genome sequencing of E. faecium P47, which had all four florfenicol and oxazolidinone resistance genes and high MIC levels for both florfenicol (256 mg/L) and linezolid (8 mg/L), revealed that it contained a chromosome and 3 plasmids (pP47-27, pP47-61, and pP47-180). The four florfenicol and oxazolidinone resistance genes were all related to the insertion sequences IS1216 and located on two smaller plasmids. The genes fexB and poxtA encoded in pP47-27, while fexA and optrA encoded in the conjugative plasmid pP47-61. Comparative analysis of homologous plasmids revealed that the sequences with high identities were plasmid sequences from various Enterococcus species except for the Tn6349 sequence from a Staphylococcus aureus chromosome (MH746818.1). The current study revealed that florfenicol and oxazolidinone resistance genes (fexA, fexB, poxtA, and optrA) were widely distributed in Enterococcus isolates from animal in China. The mobile genetic elements, including the insertion sequences and conjugative plasmid, played an important role in the horizontal transfer of florfenicol and oxazolidinone resistance.
Biocrust Amendments to Topsoils Facilitate Biocrust Restoration in a Post-mining Arid Environment
Authors: Schultz Nick L. , Sluiter Ian R. K. , Allen Geoffrey G. , Machado-de-Lima Nathali M. , Muñoz-Rojas Miriam
Published: July 2022

Soil cryptogamic biocrusts provide many ecological functions in arid zone ecosystems, though their natural reestablishment in disturbed areas is slow. Accelerating reestablishment of biocrusts may facilitate the establishment of vascular plant communities within the timeframes of restoration targets (typically 5–15 years). One technique is to inoculate the soil surface using slurries of biocrust material harvested from another site. However, this is destructive to donor sites, and hence the potential to dilute slurries will govern the feasibility of this practice at large spatial scales. We conducted a replicated experiment on a disturbed mine site to test the individual and combined effects of two strategies for accelerating soil cryptogamic biocrust reestablishment: (1) slurry inoculation using biocrust material harvested from native vegetation; and (2) the use of psyllium husk powder as a source of mucilage to bind the soil surface, and to potentially provide a more cohesive substrate for biocrust development. The experiment comprised 90 experimental plots across six treatments, including different dilutions of the biocrust slurries and treatments with and without psyllium. Over 20 months, the reestablishing crust was dominated by cyanobacteria (including Tolypothrix distorta and Oculatella atacamensis), and these established more rapidly in the inoculated treatments than in the control treatments. The inoculated treatments also maintained this cover of cyanobacteria better through prolonged adverse conditions. The dilute biocrust slurry, at 1:100 of the biocrust in the remnant vegetation, performed as well as the 1:10 slurry, suggesting that strong dilution of biocrust slurry may improve the feasibility of using this technique at larger spatial scales. Psyllium husk powder did not improve biocrust development but helped to maintain a soil physical crust through hot, dry, and windy conditions, and so the potential longer-term advantages of psyllium need to be tested.
Mechanism and kinetics of chlorpyrifos co-metabolism by using environment restoring microbes isolated from rhizosphere of horticultural crops under subtropics
Authors: Kumar Govind , Lal Shatrohan , Soni Sumit K. , Maurya Shailendra K. , Shukla Pradeep K. , Chaudhary Parul , Bhattacherjee A. K. , Garg Neelima
Published: July 2022

The indiscriminate use of organophosphate insecticide chlorpyrifos in agricultural crops causes significant soil and water pollution and poses a serious threat to the global community. In this study, a microbial consortium ERM C-1 containing bacterial strainsPseudomonas putidaT7,Pseudomonas aeruginosaM2,Klebsiella pneumoniaeM6, and a fungal strainAspergillus terreusTF1 was developed for the effective degradation of chlorpyrifos. Results revealed that microbial strains were not only utilizing chlorpyrifos (500 mg L–1) but also coupled with plant growth-promoting characteristics and laccase production. PGP traits, that is, IAA (35.53, 45.53, 25.19, and 25.53 μg mL–1), HCN (19.85, 17.85, 12.18, and 9.85 μg mL–1), and ammonium (14.73, 16.73, 8.05, and 10.87 μg mL–1) production, and potassium (49.53, 66.72, 46.14, and 52.72 μg mL–1), phosphate (52.37, 63.89, 33.33, and 71.89 μg mL–1), and zinc (29.75, 49.75, 49.12, and 57.75 μg mL–1) solubilization tests were positive for microbial strains T7, M2, M6, and TF1, respectively. The laccase activity by ERM C-1 was estimated as 37.53, 57.16, and 87.57 enzyme U mL–1after 5, 10, and 15 days of incubation, respectively. Chlorpyrifos degradation was associated with ERM C-1 and laccase activity, and the degree of enzyme activity was higher in the consortium than in individual strains. The biodegradation study with developed consortium ERM C-1 showed a decreased chlorpyrifos concentration from the 7th day of incubation (65.77% degradation) followed by complete disappearance (100% degradation) after the 30th day of incubation in the MS medium. First-order degradation kinetics with a linear model revealed a highk–dayvalue and lowt1/2value in ERM C-1. The results of HPLC and GC-MS analysis proved that consortium ERM C-1 was capable of completely removing chlorpyrifos by co-metabolism mechanism.
In vitro and intracellular inhibitory activities of nosiheptide against Mycobacterium abscessus
Authors: Zhu Rui , Yu Xia , Zhang Tingting , Kong Yaoyao , Wang Fen , Jia Junnan , Xue Yi , Huang Hairong
Published: July 2022

The high level of inherent drug resistance of Mycobacterium abscessus makes the infection caused by it very difficult to be treated. The objective of this study was to evaluate the potential of nosiheptide (NOS) as a new drug candidate for treating M. abscessus infections. The microplate AlamarBlue assay was performed to determine the minimum inhibitory concentrations (MICs) of NOS for 28 reference strains of rapidly growing mycobacteria (RGM) and 77 clinical isolates of M. abscessus. Time-kill kinetic and post-antibiotic effect (PAE) of NOS against M. abscessus was evaluated. Its bactericidal activity against M. abscessus in macrophages was determined by an intracellular colony numerating assay. NOS manifested good activity against the reference strains of RGM and M. abscessus clinical isolates in vitro. The MICs of NOS against M. abscessus clinical isolates ranged from 0.0078 to 1 μg/ml, and the MIC50 and MIC90 were 0.125 μg/ml and 0.25 μg/ml, respectively. The pattern of growth and kill by NOS against M. abscessus was moderate with apparent concentration-dependent characteristics, and the PAE value of NOS was found to be ~6 h. Furthermore, NOS had low cell toxicity against the THP-1 cell line after 48 h of exposure (IC50 = 106.9 μM). At 4 μg/ml, NOS exhibited high intracellular bactericidal activity against M. abscessus reference strains with an inhibitory rate of 66.52% ± 1.51%, comparable with that of clarithromycin at 2 μg/ml. NOS showed suitable inhibitory activities against M. abscessus in vitro and in macrophages and could be a potential drug candidate to treat M. abscessus infection.
An amateur gut microbial configuration formed in giant panda for striving to digest cellulose in bamboo: Systematic evidence from intestinal digestive enzymes, functional genes and microbial structures
Authors: Zhan Mingye , Wang Aishan , Yao Yong , Zhou Yingmin , Zhang Shu , Fu Xiaohua , Zhou Jun , Pei Enle , Wang Lei
Published: July 2022

The giant panda has been considered to maximize nutritional intake including protein and soluble carbohydrates in bamboo, but it has spent almost entire life with the high-cellulose diet. Whether giant panda is still helpless about digesting bamboo cellulose or not is always contentious among many researchers around the world. The work has systematically clarified this issue from the perspectives of digestive enzymes, functional genes, and microbial structures in giant panda gut. The intestinal cellulase activities of panda increase with bamboo consumption, performing that the endoglucanase activity of adults reaches 10-fold that of pandas first consuming bamboo. More abundance and types of microbial endoglucanase genes occur in bamboo-diet giant panda gut, and the corresponding GH5 gene cluster is still efficiently transcribed. Gut microbes possessing cellulose-degrading genes, belong to the phylum Firmicutes and some Bacteroidetes, but their structural and functional configurations are insufficient to completely degrade cellulose. Therefore, giant panda is striving to digest cellulose in bamboo, but this adaptation is incomplete. This is probably related to the short straight carnivore-like gut structure of the giant panda, preventing the colonization of some efficient functional but anaerobic-preferred flora.
Sex plays a role in the construction of epiphytic bacterial communities on the algal bodies and receptacles of Sargassum thunbergii
Authors: Wang Jing , Li Yang , Yang Zhibo , Sun Tao , Yu Xinlong , Zhao Yayun , Tang Xuexi , Xiao Hui
Published: July 2022

The community structures of epiphytic bacteria on the surface of macroalgae are closely related to their host algae, but there is a lack of research on the differences between the epiphytic bacterial communities of male and female algae and their reproductive tissues. In this study, high-throughput sequencing was used to compare epiphytic bacterial community structures on the intertidal macroalgae Sargassum thunbergii and their receptacles between male and female samples. The epiphytic bacteria on the male and female algal bodies and receptacles had similar community structures with a large number of shared bacteria, but the samples clearly clustered separately, and the abundances of dominant taxa, specific bacteria, and indicator species differed, indicating that epiphytic bacterial communities differed significantly between the male and female S. thunbergii and their receptacles. In addition, the abundance of many predicted functional genes was significantly different between epiphytic bacteria on male and female algal bodies and receptacles, especially metabolism-related genes, and the abundances of predicted functional genes of epiphytic bacteria were significantly higher on both types of male samples than on female samples. Our study confirmed that the sex of the host algae influenced the epiphytic bacterial community structures on algae and algal reproductive tissues, and this role was mainly related to the host metabolism. The results reveal the role of host plant sex in the formation of epiphytic bacterial communities. These findings are helpful for obtaining an in-depth understanding of the construction mechanism of algae-associated bacteria.
Evaluation of four primer sets for analysis of comammox communities in black soils
Authors: Bai Xin , Hu Xiaojing , Liu Junjie , Gu Haidong , Jin Jian , Liu Xiaobing , Wang Guanghua
Published: July 2022

Comammox, as a newly discovered ammonia oxidizer, urgently needs highly efficient and specific primers to detect its community structure and diversity. In this study, the performance of widely used primer set Ntsp-amoA 162F/359R and newly designed primer sets comamoA F/R, CA377f/C576r, and CB377f/C576r were evaluated, for high-throughput sequencing of comammox amoA genes in natural and arable soils sampled from two locations in the black soil region of northeast China. Results showed that, compared with the primer set comamoA F/R, primers Ntsp-amoA 162F/359R had more advantages in detecting comammox operational taxonomic unit (OTU) numbers, diversity, and community structure. The primer sets CA377f/C576r and CB377f/C576r had an advantage in detecting comammox sequences with low relative abundance. In addition, the results of the phylogenetic tree and the relative abundance of dominant OTUs showed that the comammox in the black soils of northeast China was dominated by Nitrospira Clade B. Furthermore, our study found that long-term land use reduced the alpha diversity of the comammox community, but lead to the convergent evolution of community structure. The Mantel test and canonical correspondence analysis indicated that soil NO3–-N content was the most important factor affecting the community structure of comammox. Our study provided experience accumulation for the selection of comammox primers for high-throughput sequencing in the black soil of northeast China.
Untargeted Metabolomics Sheds Light on the Secondary Metabolism of Fungi Triggered by Choline-Based Ionic Liquids
Authors: Sequeira Patrícia , Rothkegel Maika , Domingos Patrícia , Martins Isabel , Leclercq Céline C. , Renaut Jenny , Goldman Gustavo H. , Silva Pereira Cristina
Published: July 2022

Fungal secondary metabolites constitute a rich source of yet undiscovered bioactive compounds. Their production is often silent under standard laboratory conditions, but the production of some compounds can be triggered simply by altering the cultivation conditions. The usage of an organic salt – ionic liquid – as growth medium supplement can greatly impact the biosynthesis of secondary metabolites, leading to higher diversity of compounds accumulating extracellularly. This study examines if such supplements, specifically cholinium-based ionic liquids, can support the discovery of bioactive secondary metabolites across three model species: Neurospora crassa, Aspergillus nidulans, and Aspergillus fumigatus. Enriched organic extracts obtained from medium supernatant revealed high diversity in metabolites. The supplementation led apparently to increased levels of either 1-aminocyclopropane-1-carboxylate or α-aminoisobutyric acid. The extracts where bioactive against two major foodborne bacterial strains: Staphylococcus aureus and Escherichia coli. In particular, those retrieved from N. crassa cultures showed greater bactericidal potential compared to control extracts derived from non-supplemented cultures. An untargeted mass spectrometry analysis using the Global Natural Product Social Molecular Networking tool enabled to capture the chemical diversity driven by the ionic liquid stimuli. Diverse macrolides, among other compounds, were putatively associated with A. fumigatus; whereas an unexpected richness of cyclic (depsi)peptides with N. crassa. Further studies are required to understand if the identified peptides are the major players of the bioactivity of N. crassa extracts, and to decode their biosynthesis pathways as well.
Autotoxin affects the rhizosphere microbial community structure by influencing the secretory characteristics of grapevine roots
Authors: Liu Qianwen , Zhang Liheng , Wang Lu , Wu Qingchun , Li Kun , Guo Xiuwu
Published: July 2022

Autotoxins secreted by roots into the soil can trigger rhizosphere microecological imbalances and affect root secretory properties resulting in conditions such as replanting disease. However, information on the effect of autotoxins on root secretion characteristics and regulation of the composition of rhizosphere microorganisms by altered root exudates is limited. In this study, autotoxin ρ-hydroxybenzoic acid (4-HBA) was added to the soil of potted grapevine seedlings, CO2 pulse-labeling, and DNA stable isotope probing were used to track the rhizosphere microbiome that assimilates root exudates. Bacterial and fungal microbiomes that assimilated plant-derived carbon were identified by high-throughput sequencing. Results showed that 4-HBA treatment altered bacterial and fungal communities in 13C-labeled organisms, with a lower abundance of beneficial bacteria (e.g., Gemmatimonas, Streptomyces, and Bacillus) and a higher abundance of potential pathogen fungi (e.g., Fusarium, Neocosmospora, Gibberella, and Fusicolla) by changing the composition of root exudates. The exogenous addition of upregulated compound mixtures of root exudates reduced the abundance of beneficial bacterial Bacillus and increased the abundance of potential pathogen fungi Gibberella. These results suggest that 4-HBA can alter root secretion properties and altered root exudates may enrich certain potential pathogens and reduce certain beneficial bacteria, thereby unbalancing the structure of the rhizosphere microbial community.
Identification of gut metabolites associated with Parkinson’s disease using bioinformatic analyses
Authors: Yan Jun , Feng Xia , Zhou Xia , Zhao Mengjie , Xiao Hong , Li Rui , Shen Hong
Published: July 2022

Background

Parkinson’s disease (PD) is a common neurodegenerative disease affecting the movement of elderly patients. Environmental exposures are the risk factors for PD; however, gut environmental risk factors for PD are critically understudied. The proof-of-concept study is to identify gut metabolites in feces, as environmental exposure risk factors, that are associated with PD and potentially increase the risk for PD by using leverage of known toxicology results.

Materials and methods

We collected the data regarding the gut metabolites whose levels were significantly changed in the feces of patients with PD from the original clinical studies after searching the following databases: EBM Reviews, PubMed, Embase, MEDLINE, and Elsevier ClinicalKey. We further searched each candidate metabolite-interacting PD gene set by using the public Comparative Toxicogenomics Database (CTD), identified and validated gut metabolites associated with PD, and determined gut metabolites affecting specific biological functions and cellular pathways involved in PD by using PANTHER tools.

Results

Sixteen metabolites were identified and divided into the following main categories according to their structures and biological functions: alcohols (ethanol), amino acids (leucine, phenylalanine, pyroglutamic acid, glutamate, and tyrosine), short-chain fatty acids (propionate and butyrate), unsaturated fatty acids (linoleic acid and oleic acid), energy metabolism (lactate, pyruvate, and fumarate), vitamins (nicotinic acid and pantothenic acid), and choline metabolism (choline). Finally, a total of three identified metabolites, including butyrate, tyrosine, and phenylalanine, were validated that were associated with PD.

Conclusion

Our findings identified the gut metabolites that were highly enriched for PD genes and potentially increase the risk of developing PD. The identification of gut metabolite exposures can provide biomarkers for disease identification, facilitate an understanding of the relationship between gut metabolite exposures and response, and present an opportunity for PD prevention and therapies.
Sex Differences in Hypothalamic Changes and the Metabolic Response of TgAPP Mice to a High Fat Diet
Authors: Freire-Regatillo Alejandra , Diaz-Pacheco Sonia , Frago Laura M. , Arévalo María-Ángeles , Argente Jesús , Garcia-Segura Luis M. , de Ceballos María L. , Chowen Julie A.
Published: July 2022

The propensity to develop neurodegenerative diseases is influenced by diverse factors including genetic background, sex, lifestyle, including dietary habits and being overweight, and age. Indeed, with aging, there is an increased incidence of obesity and neurodegenerative processes, both of which are associated with inflammatory responses, in a sex-specific manner. High fat diet (HFD) commonly leads to obesity and markedly affects metabolism, both peripherally and centrally. Here we analyzed the metabolic and inflammatory responses of middle-aged (11–12 months old) transgenic amyloid precursor protein (TgAPP) mice of both sexes to HFD for 18 weeks (starting at 7–8 months of age). We found clear sex differences with females gaining significantly more weight and fat mass than males, with a larger increase in circulating leptin levels and expression of inflammatory markers in visceral adipose tissue. Glycemia and insulin levels increased in HFD fed mice of both sexes, with TgAPP mice being more affected than wild type (WT) mice. In the hypothalamus, murine amyloid β (Aβ) levels were increased by HFD intake exclusively in males, reaching statistical significance in TgAPP males. On a low fat diet (LFD), TgAPP males had significantly lower mRNA levels of the anorexigenic neuropeptide proopiomelanocortin (POMC) than WT males, with HFD intake decreasing the expression of the orexigenic neuropeptides Agouti-related peptide (AgRP) and neuropeptide Y (NPY), especially in TgAPP mice. In females, HFD increased POMC mRNA levels but had no effect on AgRP or NPY mRNA levels, and with no effect on genotype. There was no effect of diet or genotype on the hypothalamic inflammatory markers analyzed or the astrogliosis marker glial acidic protein (GFAP); however, levels of the microglial marker Iba-1 increased selectively in male TgAPP mice. In summary, the response to HFD intake was significantly affected by sex, with fewer effects due to genotype. Hypothalamic inflammatory cytokine expression and astrogliosis were little affected by HFD in middle-aged mice, although in TgAPP males, which showed increased Aβ, there was microglial activation. Thus, excess intake of diets high in fat should be avoided because of its possible detrimental consequences.
UWB indoor positioning optimization algorithm based on genetic annealing and clustering analysis
Authors: Guo Hua , Li Mengqi , Zhang Xuejing , Gao Xiaotian , Liu Qian
Published: July 2022

Indoor location information is an indispensable parameter for modern intelligent warehouse management and robot navigation. Indoor wireless positioning exhibits large errors due to factors such as indoor non-line-of-sight (NLOS) obstructions. In the present study, the error value under the time of arrival (TOA) algorithm was evaluated, and the trilateral positioning method was optimized to minimize the errors. An optimization algorithm for indoor ultra-wideband (UWB) positioning was designed, which was referred as annealing evolution and clustering fusion optimization algorithm. The algorithm exploited the good local search capability of the simulated annealing algorithm and the good global search capability of the genetic algorithm to optimize cluster analysis. The optimal result from sampled data was quickly determined to achieve effective and accurate positioning. These features reduced the non-direct aiming error in the indoor UWB environment. The final experimental results showed that the optimized algorithm significantly reduced noise interference as well as improved positioning accuracy in an NLOS indoor environment with less than 10 cm positioning error.
Longitudinal ventricular cerebrospinal fluid profile in patients with spontaneous subarachnoid hemorrhage
Authors: Zinganell Anne , Bsteh Gabriel , Di Pauli Franziska , Rass Verena , Helbok Raimund , Walde Janette , Deisenhammer Florian , Hegen Harald
Published: July 2022

Background

Spontaneous subarachnoid hemorrhage (SAH) is a severe neurological disease that frequently requires placement of external ventricular drainage (EVD). Cerebrospinal fluid (CSF) obtained via the drain is used to detect potential complications of SAH.

Objective

This study aimed to describe the longitudinal profile of routine CSF parameters in patients with SAH and to identify associations with neurological complications.

Methods

A total of thirty-three patients with spontaneous SAH who required an EVD and had at least three consecutive CSF samples collected over a period of more than 7 days were included in this study.

Results

A median of 6 longitudinally collected CSF samples per patient were available within 1–22 days after SAH onset. Overall, red blood cells (RBC) steadily decreased over time, whereas white blood cells (WBC) and total protein (TP) increased until days 6 and 13, respectively, and decreased thereafter. The estimated decay rates of RBC, WBC, and TP were 28, 22, and 6% per day. Distinct CSF patterns over time were linked to known complications after SAH. Patients with rebleeding showed increased RBC, TP, and phagocytosing cells compared to patients without re-bleeding. For ventriculitis, an elevated cell index with a higher proportion of granulocytes was characteristic. CSF of patients with delayed cerebral ischemia showed increased RBC and WBC compared to patients without DCI. Early CSF WBC and cell index were predictive for the occurrence of DCI and ventriculitis later during the disease course. The amount of daily CSF drainage via EVD had no impact on routine CSF parameters.

Conclusion

Longitudinal CSF characteristics are associated with SAH-related complications.
Chronic anemia: The effects on the connectivity of white matter
Authors: González-Zacarías Clio , Choi Soyoung , Vu Chau , Xu Botian , Shen Jian , Joshi Anand A. , Leahy Richard M. , Wood John C.
Published: July 2022

Chronic anemia is commonly observed in patients with hemoglobinopathies, mainly represented by disorders of altered hemoglobin (Hb) structure (sickle cell disease, SCD) and impaired Hb synthesis (e.g. thalassemia syndromes, non-SCD anemia). Both hemoglobinopathies have been associated with white matter (WM) alterations. Novel structural MRI research in our laboratory demonstrated that WM volume was diffusely lower in deep, watershed areas proportional to anemia severity. Furthermore, diffusion tensor imaging analysis has provided evidence that WM microstructure is disrupted proportionally to Hb level and oxygen saturation. SCD patients have been widely studied and demonstrate lower fractional anisotropy (FA) in the corticospinal tract and cerebellum across the internal capsule and corpus callosum. In the present study, we compared 19 SCD and 15 non-SCD anemia patients with a wide range of Hb values allowing the characterization of the effects of chronic anemia in isolation of sickle Hb. We performed a tensor analysis to quantify FA changes in WM connectivity in chronic anemic patients. We calculated the volumetric mean of FA along the pathway of tracks connecting two regions of interest defined by BrainSuite's BCI-DNI atlas. In general, we found lower FA values in anemic patients; indicating the loss of coherence in the main diffusion direction that potentially indicates WM injury. We saw a positive correlation between FA and hemoglobin in these same regions, suggesting that decreased WM microstructural integrity FA is highly driven by chronic hypoxia. The only connection that did not follow this pattern was the connectivity within the left middle-inferior temporal gyrus. Interestingly, more reductions in FA were observed in non-SCD patients (mainly along with intrahemispheric WM bundles and watershed areas) than the SCD patients (mainly interhemispheric).
Evaluation of decompressive craniectomy in mice after severe traumatic brain injury
Authors: Liu Yuheng , Liu Xuanhui , Chen Zhijuan , Wang Yuanzhi , Li Jing , Gong Junjie , He Anqi , Zhao Mingyu , Yang Chen , Yang Weidong , Wang Zengguang
Published: July 2022

Decompressive craniectomy (DC) is of great significance for relieving acute intracranial hypertension and saving lives after traumatic brain injury (TBI). In this study, a severe TBI mouse model was created using controlled cortical impact (CCI), and a surgical model of DC was established. Furthermore, a series of neurological function assessments were performed to better understand the pathophysiological changes after DC. In this study, mice were randomly allocated into three groups, namely, CCI group, CCI+DC group, and Sham group. The mice in the CCI and CCI+DC groups received CCI after opening a bone window, and after brain injury, immediately returned the bone window to simulate skull condition after a TBI. The CCI+DC group underwent DC and contused tissue removal 6 h after CCI. The mice in the CCI group underwent the same anesthesia process; however, no further treatment of the bone window and trauma was performed. The mice in the Sham group underwent anesthesia and the process of opening the skin and bone window, but not in the CCI group. Changes in Modified Neurological Severity Score, rotarod performance, Morris water maze, intracranial pressure (ICP), cerebral blood flow (CBF), brain edema, blood–brain barrier (BBB), inflammatory factors, neuronal apoptosis, and glial cell expression were evaluated. Compared with the CCI group, the CCI+DC group had significantly lower ICP, superior neurological and motor function at 24 h after injury, and less severe BBB damage after injury. Most inflammatory cytokine expressions and the number of apoptotic cells in the brain tissue of mice in the CCI+DC group were lower than in the CCI group at 3 days after injury, with markedly reduced astrocyte and microglia expression. However, the degree of brain edema in the CCI+DC group was greater than in the CCI group, and neurological and motor functions, as well as spatial cognitive and learning ability, were significantly poorer at 14 days after injury.
The Frequency of V122I Transthyretin Mutation in a Cohort of African American Individuals With Bilateral Carpal Tunnel Syndrome
Authors: Shije Jeffrey Z. , Bautista Maria A. B. , Smotherman Carmen
Published: July 2022

Introduction

Hereditary transthyretin amyloidosis (hATTR) can cause multisystem organ disorders including polyneuropathy and cardiomyopathy. Amongst the many known pathologic mutations of the transthyretin (TTR) gene, the Val122Ile (V122I) mutation can be found in 3–4% of African Americans. Up to 47% of patients with the V122I hATTR cardiomyopathy had a history of carpal tunnel syndrome (CTS). This raises the question should we screen for this mutation in African Americans with bilateral CTS for the purpose of preventing advanced disease associated with hATTR. This is a prospective pilot study to determine the likelihood of African Americans with bilateral CTS having the V122I mutation and whether various clinical factors contribute to that probability.

Methodology

Adult African American patients without prior history of amyloidosis diagnosed with bilateral CTS were recruited for the study. They received genetic testing to screen for a TTR mutation. They also completed questionnaires to screen for symptoms of cardiomyopathy and neuropathy, other risk factors for CTS, and family history of CTS and cardiomyopathy.

Result

Two of the sixteen patients (12.5%) in this cohort were found to have the V122I mutation. The absence of polyneuropathy and cardiomyopathy symptoms, presence of other CTS risk factors, and absence of family history of CTS and cardiomyopathy did not decrease the likelihood of V122I mutation in this cohort.

Conclusion

The frequency of V122I transthyretin mutation in African Americans with bilateral CTS may be higher than 3–4%. The presence of bilateral CTS alone may be a justification to screen for TTR mutation in this population.
Reproducing FSL's fMRI data analysis via Nipype: Relevance, challenges, and solutions
Authors: Chen Yibei , Hopp Frederic R. , Malik Musa , Wang Paula T. , Woodman Kylie , Youk Sungbin , Weber René
Published: July 2022

The “replication crisis” in neuroscientific research has led to calls for improving reproducibility. In traditional neuroscience analyses, irreproducibility may occur as a result of issues across various stages of the methodological process. For example, different operating systems, different software packages, and even different versions of the same package can lead to variable results. Nipype, an open-source Python project, integrates different neuroimaging software packages uniformly to improve the reproducibility of neuroimaging analyses. Nipype has the advantage over traditional software packages (e.g., FSL, ANFI, SPM, etc.) by (1) providing comprehensive software development frameworks and usage information, (2) improving computational efficiency, (3) facilitating reproducibility through sufficient details, and (4) easing the steep learning curve. Despite the rich tutorials it has provided, the Nipype community lacks a standard three-level GLM tutorial for FSL. Using the classical Flanker task dataset, we first precisely reproduce a three-level GLM analysis with FSL via Nipype. Next, we point out some undocumented discrepancies between Nipype and FSL functions that led to substantial differences in results. Finally, we provide revised Nipype code in re-executable notebooks that assure result invariability between FSL and Nipype. Our analyses, notebooks, and operating software specifications (e.g., docker build files) are available on the Open Science Framework platform.
Altered insular functional connectivity correlates to impaired vigilant attention after sleep deprivation: A resting-state functional magnetic resonance imaging study
Authors: Fu Weiwei , Dai Cimin , Chen Jie , Wang Letong , Song Tao , Peng Ziyi , Xu Mengmeng , Xu Lin , Tang Yuguo , Shao Yongcong
Published: July 2022

Objectives

This study used resting-state functional magnetic resonance imaging (rs-fMRI) scans to assess the dominant effects of 36 h total sleep deprivation (TSD) on vigilant attention and changes in the resting-state network.

Materials and methods

Twenty-two healthy college students were enrolled in this study. Participants underwent two rs-fMRI scans, once in rested wakefulness (RW) and once after 36 h of TSD. We used psychomotor vigilance tasks (PVT) to measure vigilant attention. The region-of-interest to region-of-interest correlation was employed to analyze the relationship within the salience network (SN) and between other networks after 36 h of TSD. Furthermore, Pearson’s correlation analysis investigated the relationship between altered insular functional connectivity and PVT performance.

Results

After 36 h of TSD, participants showed significantly decreased vigilant attention. Additionally, TSD induced decreased functional connectivity between the visual and parietal regions, whereas, a significant increase was observed between the anterior cingulate cortex and insula. Moreover, changes in functional connectivity in the anterior cingulate cortex and insula showed a significant positive correlation with the response time to PVT.

Conclusion

Our results suggest that 36 h of TSD impaired vigilant visual attention, resulting in slower reaction times. The decrease in visual-parietal functional connectivity may be related to the decrease in the reception of information in the brain. Enhanced functional connectivity of the anterior cingulate cortex with the insula revealed that the brain network compensation occurs mainly in executive function.