bluuebunny/crossref_metadata_2025 huggingface dataset:
Improving sightings-derived residency estimation for whale shark aggregations: A novel metric applied to a global data set
Authors: Araujo Gonzalo , Agustines Ariana , Bach Steffen S. , Cochran Jesse E. M. , Parra-Galván Emilio de la , Parra-Venegas Rafael de la , Diamant Stella , Dove Alistair , Fox Steve , Graham Rachel T. , Green Sofia M. , Green Jonathan R. , Hardenstine Royale S. , Hearn Alex , Himawan Mahardika R. , Hobbs Rhys , Holmberg Jason , Shameel Ibrahim , Jaidah Mohammed Y. , Labaja Jessica , Leblond Savi , Legaspi Christine G. , Maguiño Rossana , Magson Kirsty , Marcoux Stacia D. , Marcoux Travis M. , Marley Sarah Anne , Matalobos Meynard , Mendoza Alejandra , Miranda Joni A. , Norman Brad M. , Perry Cameron T. , Pierce Simon J. , Ponzo Alessandro , Prebble Clare E. M. , Ramírez-Macías Dení , Rees Richard , Reeve-Arnold Katie E. , Reynolds Samantha D. , Robinson David P. , Rohner Christoph A. , Rowat David , Snow Sally , Vázquez-Haikin Abraham , Watts Alex M.
Published: July 2022

The world’s largest extant fish, the whale shark Rhincodon typus, is one of the most-studied species of sharks globally. The discovery of predictable aggregation sites where these animals gather seasonally or are sighted year-round – most of which are coastal and juvenile-dominated – has allowed for a rapid expansion of research on this species. The most common method for studying whale sharks at these sites is photographic identification (photo-ID). This technique allows for long-term individual-based data to be collected which can, in turn, be used to evaluate population structure, build population models, identify long-distance movements, and assess philopatry and other population dynamics. Lagged identification rate (LIR) models have fewer underlying assumptions than more traditional capture mark recapture approaches, making them more broadly applicable to marine taxa, especially far-ranging megafauna species like whale sharks. However, the increased flexibility comes at a cost. Parameter estimations based on LIR can be difficult to interpret and may not be comparable between areas with different sampling regimes. Using a unique data-set from the Philippines with ~8 years of nearly continuous survey effort, we were able to derive a metric for converting LIR residency estimates into more intuitive days-per-year units. We applied this metric to 25 different sites allowing for the first quantitatively-meaningful comparison of sightings-derived residence among the world’s whale shark aggregations. We validated these results against the only three published acoustic residence metrics (falling within the ranges established by these earlier works in all cases). The results were then used to understand residency behaviours exhibited by the sharks at each site. The adjusted residency metric is an improvement to LIR-based population modelling, already one of the most widely used tools for describing whale shark aggregations. The standardised methods presented here can serve as a valuable tool for assessing residency patterns of whale sharks, which is crucial for tailored conservation action, and can cautiously be tested in other taxa.
Recreational Fishing Impacts in an Offshore and Deep-Water Marine Park: Examining Patterns in Fished Species Using Hybrid Frequentist Model Selection and Bayesian Inference
Authors: Aston Charlotte , Langlois Tim , Fisher Rebecca , Monk Jacquomo , Gibbons Brooke , Giraldo-Ospina Anita , Lawrence Emma , Keesing John , Lebrec Ulysse , Babcock Russ C.
Published: July 2022

No-take marine reserves are often located in remote locations far away from human activity, limiting perceived impact on extractive users but also reducing their use for investigating impacts of fishing. This study aimed to establish a benchmark in the distribution of fished species across the Ningaloo Marine Park – Commonwealth (NMP-Commonwealth), and adjacent comparable habitats within the Ningaloo Marine Park - State (NMP-State), in Western Australia to test if there was evidence of an effect of recreational fishing, as no commercial fishing is allowed within either marine park. We also examined whether the remote location of the newly established (2018) No-take Zone (NTZ), in NMP-Commonwealth, limits its use for studying the effects of fishing. Throughout the NMP-Commonwealth and NMP-State, where recreational fishing is permitted, we expected the abundance of recreationally fished fish species to increase with increasing distance to the nearest boat ramp, as a proxy of recreational fishing effort. Conversely, we did not expect the abundance of non-fished species and overall species richness to vary in response to the proxy for human activity. Distance to the nearest boat ramp was found to be a strong predictor of fished species abundance, indicating that the effect of recreational fishing can be detected across the NMP-Commonwealth. The effect of the NTZ on fished species abundance was weakly positive, but this difference across the NTZ is expected to increase over time. Habitat composition predictors were only found to influence species richness and non-fished species abundance. This study suggests a clear footprint of recreational fishing across the NMP-Commonwealth and as a result the new NTZ, despite its remote location, can act as a control in future studies of recreational fishing effects.
Review of the concentration, bioaccumulation, and effects of lanthanides in marine systems
Authors: Neira Patricia , Romero-Freire Ana , Basallote María Dolores , Qiu Hao , Cobelo-García Antonio , Cánovas Carlos Ruiz
Published: July 2022

Rare earth elements (REEs) or lanthanides are often found together in nature, and they are used in multiple anthropogenic activities from green energy and medical technologies to telecommunications and defense systems. However, the current understanding on the concentration and behavior of REEs in oceans and marine organisms is limited, and no regulatory information or limits have been settled. Here, we present a review of the concentrations of lanthanides in marine waters and biota. REEs reach aquatic ecosystems mainly by continental contributions, and the maximum reported concentrations of REEs are found on the platform surface near the coast due to their continental origin. For coastal waters, we find maximum REE levels in the surface water that decrease with depth until a certain stability. Their concentrations diminish as they move toward the open ocean, where concentrations tend to increase vertically with depth in the water column. Only cerium (Ce) showed different patterns from other REEs caused by Ce different redox states: III and IV, reflecting the oxidation of dissolved Ce (III) to particulate Ce (IV) when reacting with the O2 to form CeO2. In seawater, heavy REEs tend to remain in solution forming complexes usually unavailable for organisms, while light REEs are most likely to be assimilated by them, posing potential biological implications. Bioaccumulation of REEs decreases as marine trophic level increases, showing a trophic dilution pattern. Generally, higher concentrations are found in organisms such as phytoplankton, zooplankton, and algae species, while the lowest concentrations are found in mollusks, corals, and fish species. According to the current trend in the REE industry, the increasing anthropogenic emissions are a fact; therefore, more studies will be needed regarding their fractionation, the transformation processes with which they become bioavailable, and their pathways in marine systems.
Effect of cyclonic storm Vardah on the community structure and ecosystem functioning of macrobenthic fauna in the intertidal region of South Andaman Islands
Authors: Sahu Nosad , Lakra Raj Kiran , Thiruchitrambalam Ganesh
Published: July 2022

An investigation was carried out to understand the effect of a cyclone Vardah on the functioning of macrobenthos. The assessment was accomplished by comparing before cyclone (BC) and after cyclone (AC) data of macrobenthos. Additionally, temporal changes in the faunal assemblages were evident through multivariate techniques. Five distinguished assemblages could be noticed through the Bray–Curtis similarity representing different phases of the cyclone. The cyclonic effect also resulted in the recruitment of some macrobenthic species and the loss of a few during the study period. Biological trait analysis identified subsurface deposit feeders, upward and downward conveyers, Ecological Group IV, mid-mobile macrobenthos and size class of 2–4 cm as the important groups that dominated the functioning of the macrobenthic community immediately after the cyclone. The resilience and recruitment of macrobenthos were explained using functional redundancy.
Using random forest algorithm for glomerular and tubular injury diagnosis
Authors: Song Wenzhu , Zhou Xiaoshuang , Duan Qi , Wang Qian , Li Yaheng , Li Aizhong , Zhou Wenjing , Sun Lin , Qiu Lixia , Li Rongshan , Li Yafeng
Published: July 2022

Objectives

Chronic kidney disease (CKD) is a common chronic condition with high incidence and insidious onset. Glomerular injury (GI) and tubular injury (TI) represent early manifestations of CKD and could indicate the risk of its development. In this study, we aimed to classify GI and TI using three machine learning algorithms to promote their early diagnosis and slow the progression of CKD.

Methods

Demographic information, physical examination, blood, and morning urine samples were first collected from 13,550 subjects in 10 counties in Shanxi province for classification of GI and TI. Besides, LASSO regression was employed for feature selection of explanatory variables, and the SMOTE (synthetic minority over-sampling technique) algorithm was used to balance target datasets, i.e., GI and TI. Afterward, Random Forest (RF), Naive Bayes (NB), and logistic regression (LR) were constructed to achieve classification of GI and TI, respectively.

Results

A total of 12,330 participants enrolled in this study, with 20 explanatory variables. The number of patients with GI, and TI were 1,587 (12.8%) and 1,456 (11.8%), respectively. After feature selection by LASSO, 14 and 15 explanatory variables remained in these two datasets. Besides, after SMOTE, the number of patients and normal ones were 6,165, 6,165 for GI, and 6,165, 6,164 for TI, respectively. RF outperformed NB and LR in terms of accuracy (78.14, 80.49%), sensitivity (82.00, 84.60%), specificity (74.29, 76.09%), and AUC (0.868, 0.885) for both GI and TI; the four variables contributing most to the classification of GI and TI represented SBP, DBP, sex, age and age, SBP, FPG, and GHb, respectively.

Conclusion

RF boasts good performance in classifying GI and TI, which allows for early auxiliary diagnosis of GI and TI, thus facilitating to help alleviate the progression of CKD, and enjoying great prospects in clinical practice.
The dynamic transcriptome during maturation of biofilms formed by methicillin-resistant Staphylococcus aureus
Authors: Vlaeminck Jelle , Lin Qiang , Xavier Basil Britto , De Backer Sarah , Berkell Matilda , De Greve Henri , Hernalsteens Jean-Pierre , Kumar-Singh Samir , Goossens Herman , Malhotra-Kumar Surbhi
Published: July 2022

Background

Methicillin-resistantStaphylococcus aureus(MRSA), a leading cause of chronic infections, forms prolific biofilms which afford an escape route from antibiotic treatment and host immunity. However, MRSA clones are genetically diverse, and mechanisms underlying biofilm formation remain under-studied. Such studies form the basis for developing targeted therapeutics. Here, we studied the temporal changes in the biofilm transcriptome of three pandemic MRSA clones: USA300, HEMRSA-15, and ST239.

Methods

Biofilm formation was assessed using a static model with one representative strain per clone. Total RNA was extracted from biofilm and planktonic cultures after 24, 48, and 72 h of growth, followed by rRNA depletion and sequencing (Illumina Inc., San Diego, CA, United States, NextSeq500, v2, 1 × 75 bp). Differentially expressed gene (DEG) analysis between phenotypes and among early (24 h), intermediate (48 h), and late (72 h) stages of biofilms was performed together within silicoco-expression network construction and compared between clones. To understand the influence of SCCmecand ACME on biofilm formation, isogenic mutants containing deletions of the entire elements or of single genes therein were constructed in USA300.

Results

Genes involved in primarily core genome-encoded KEGG pathways (transporters and others) were upregulated in 24-h biofilm culture compared to 24-h planktonic culture. However, the number of affected pathways in the ST239 24 h biofilm (n= 11) was remarkably lower than that in USA300/EMRSA-15 biofilms (USA300:n= 27, HEMRSA-15:n= 58). TheclfAgene, which encodes clumping factor A, was the single common DEG identified across the three clones in 24-h biofilm culture (2.2- to 2.66-fold). In intermediate (48 h) and late (72 h) stages of biofilms, decreased expression of central metabolic and fermentative pathways (glycolysis/gluconeogenesis, fatty acid biosynthesis), indicating a shift to anaerobic conditions, was already evident in USA300 and HEMRSA-15 in 48-h biofilm cultures; ST239 showed a similar profile at 72 h. Last, SCCmec+ACME deletion andopp3Ddisruption negatively affected USA300 biofilm formation.

Conclusion

Our data show striking differences in gene expression during biofilm formation by three of the most important pandemic MRSA clones, USA300, HEMRSA-15, and ST239. TheclfAgene was the only significantly upregulated gene across all three strains in 24-h biofilm cultures and exemplifies an important target to disrupt early biofilms. Furthermore, our data indicate a critical role for arginine catabolism pathways in early biofilm formation.
Toxic/Bioactive Peptide Synthesis Genes Rearranged by Insertion Sequence Elements Among the Bloom-Forming Cyanobacteria Planktothrix
Authors: Entfellner Elisabeth , Li Ruibao , Jiang Yiming , Ru Jinlong , Blom Jochen , Deng Li , Kurmayer Rainer
Published: July 2022

It has been generally hypothesized that mobile elements can induce genomic rearrangements and influence the distribution and functionality of toxic/bioactive peptide synthesis pathways in microbes. In this study, we performed in depth genomic analysis by completing the genomes of 13 phylogenetically diverse strains of the bloom-forming freshwater cyanobacteria Planktothrix spp. to investigate the role of insertion sequence (IS) elements in seven pathways. Chromosome size varied from 4.7–4.8 Mbp (phylogenetic Lineage 1 of P. agardhii/P. rubescens thriving in shallow waterbodies) to 5.4–5.6 Mbp (Lineage 2 of P. agardhii/P. rubescens thriving in deeper physically stratified lakes and reservoirs) and 6.3–6.6 Mbp (Lineage 3, P. pseudagardhii/P. tepida including planktic and benthic ecotypes). Although the variation in chromosome size was positively related to the proportion of IS elements (1.1–3.7% on chromosome), quantitatively, IS elements and other paralogs only had a minor share in chromosome size variation. Thus, the major part of genomic variation must have resulted from gene loss processes (ancestor of Lineages 1 and 2) and horizontal gene transfer (HGT). Six of seven peptide synthesis gene clusters were found located on the chromosome and occurred already in the ancestor of P. agardhii/P. rubescens, and became partly lost during evolution of Lineage 1. In general, no increased IS element frequency in the vicinity of peptide synthesis gene clusters was observed. We found a higher proportion of IS elements in ten breaking regions related to chromosomal rearrangements and a tendency for colocalization of toxic/bioactive peptide synthesis gene clusters on the chromosome.
Burkholderia ambifaria XN08: A plant growth-promoting endophytic bacterium with biocontrol potential against sharp eyespot in wheat
Authors: An Chao , Ma Saijian , Liu Chen , Ding Hao , Xue Wenjiao
Published: July 2022

Plant growth-promoting bacteria (PGPB) have been considered promising biological agents to increase crop yields for years. However, the successful application of PGPB for biocontrol of sharp eyespot in wheat has been limited, partly by the lack of knowledge of the ecological/environmental factors affecting the colonization, prevalence, and activity of beneficial bacteria on the crop. In this study, an endophytic bacterium XN08 with antagonistic activity against Rhizoctonia cerealis (wheat sharp eyespot pathogenic fungus), isolated from healthy wheat plants, was identified as Burkholderia ambifaria according to the sequence analysis of 16S rRNA. The antibiotic synthesis gene amplification and ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-QTOF-MS) analyses were used to characterize the secondary metabolites. The results showed that the known powerful antifungal compound named pyrrolnitrin was produced by the strain XN08. In addition, B. ambifaria XN08 also showed the capacity for phosphate solubilization, indole-3-acetic acid (IAA), protease, and siderophore production in vitro. In the pot experiments, a derivate strain carrying the green fluorescent protein (GFP) gene was used to observe its colonization in wheat plants. The results showed that GFP-tagged B. ambifaria could colonize wheat tissues effectively. This significant colonization was accompanied by an enhancement of wheat plants' growth and an induction of immune resistance for wheat seedlings, which was revealed by the higher activities of polyphenol oxidase (PPO), peroxidase (POD), and phenylalanine ammonia-lyase (PAL). As far as we know, this is the first report describing the colonization traits of B. ambifaria in wheat plants. In addition, our results indicated that B. ambifaria XN08 might serve as a new effective biocontrol agent against wheat sharp eyespot disease caused by R. cerealis.
The ABCT31 Transporter Regulates the Export System of Phenylacetic Acid as a Side-Chain Precursor of Penicillin G in Monascus ruber M7
Authors: Ramzan Rabia , Virk Muhammad Safiullah , Chen Fusheng
Published: July 2022

The biosynthesis of penicillin G (PG) is compartmentalized, and the transportation of the end and intermediate products, and substrates (precursors) such as L-cysteine (L-Cys), L-valine (L-Val) and phenylacetic acid (PAA) requires traversing membrane barriers. However, the transportation system of PAA as a side chain of PG are unclear yet. To discover ABC transporters (ABCTs) involved in the transportation of PAA, the expression levels of 38 ABCT genes in the genome of Monascus ruber M7, culturing with and without PAA, were examined, and found that one abct gene, namely abct31, was considerably up-regulated with PAA, indicating that abct31 may be relative with PAA transportation. Furthermore the disruption of abct31 was carried out, and the effects of two PG substrate's amino acids (L-Cys and L-Val), PAA and some other weak acids on the morphologies and production of secondary metabolites (SMs) of Δabct31 and M. ruber M7, were performed through feeding experiments. The results revealed that L-Cys, L-Val and PAA substantially impacted the morphologies and SMs production of Δabct31 and M. ruber M7. The UPLC-MS/MS analysis findings demonstrated that Δabct31 did not interrupt the synthesis of PG in M. ruber M7. According to the results, it suggests that abct31 is involved in the resistance and detoxification of the weak acids, including the PAA in M. ruber M7.
Complete Genome Sequences of One Salt-Tolerant and Petroleum Hydrocarbon-Emulsifying Terribacillus saccharophilus Strain ZY-1
Authors: Su Zhaoying , Yang Shicheng , Li Mingchang , Chen Yu , Wang Shaojing , Yun Yuan , Li Guoqiang , Ma Ting
Published: July 2022

Salt tolerance is one of the most important problems in the field of environmental governance and restoration. Among the various sources of factors, except temperature, salinity is a key factor that interrupts bacterial growth significantly. In this regard, constant efforts are made for the development of salt-tolerant strains, but few strains with salt tolerance, such as Terribacillus saccharophilus, were found, and there are still few relevant reports about their salt tolerance from complete genomic analysis. Furthermore, with the development of the economy, environmental pollution caused by oil exploitation has attracted much attention, so it is crucial to find the bacteria from T. saccharophilus which could degrade petroleum hydrocarbon even under high-salt conditions. Herein, one T. saccharophilus strain named ZY-1 with salt tolerance was isolated by increasing the salinity on LB medium step by step with reservoir water as the bacterial source. Its complete genome was sequenced, which was the first report of the complete genome for T. saccharophilus species with petroleum hydrocarbon degradation and emulsifying properties. In addition, its genome sequences were compared with the other five strains that are from the same genus level. The results indicated that there really exist some differences among them. In addition, some characteristics were studied. The salt-tolerant strain ZY-1 developed in this study and its emulsification and degradation performance of petroleum hydrocarbons were studied, which is expected to widely broaden the research scope of petroleum hydrocarbon-degrading bacteria in the oil field environment even in the extreme environment. The experiments verified that ZY-1 could significantly grow not only in the salt field but also in the oil field environment. It also demonstrated that the developed salt-tolerant strain can be applied in the petroleum hydrocarbon pollution field for bioremediation. In addition, we expect that the identified variants which occurred specifically in the high-salt strain will enhance the molecular biological understanding and be broadly applied to the biological engineering field.
Polyhydroxybutyrate-producing cyanobacteria from lampenflora: The case study of the “Stiffe” caves in Italy
Authors: Djebaili Rihab , Mignini Amedeo , Vaccarelli Ilaria , Pellegrini Marika , Spera Daniela M. , Del Gallo Maddalena , D’Alessandro Anna Maria
Published: July 2022

This study aimed to estimate the green formation lampenflora of “Stiffe” caves in order to evaluate their suitability as an isolation source of cyanobacteria useful for the production of polyhydroxyalkanoates (PHAs). The cave system was chosen as the sampling site due to its touristic use and the presence of high-impact illuminations. The biofilms and the mats of the illuminated walls were sampled. Samples were investigated by 16S rRNA gene analysis and culturable cyanobacteria isolation. The isolated strains were then screened for the production of PHAs under typical culturing and nutritional starvation. Cultures were checked for PHA accumulation, poly-β-hydroxybutyrate (PHB) presence (infrared spectroscopy), and pigment production. The 16S rRNA gene metabarcoding. Highlighted a considerable extent of the pressure exerted by anthropogenic activities. However, the isolation yielded eleven cyanobacteria isolates with good PHA (mainly PHB)-producing abilities and interesting pigment production rates (chlorophyll a and carotenoids). Under normal conditions (BG110), the accumulation abilities ranged from 266 to 1,152 ng mg dry biomass–1. The optimization of bioprocesses through nutritional starvation resulted in a 2.5-fold increase. Fourier transform infrared (FTIR) studies established the occurrence of PHB within PHAs extracted by cyanobacteria isolates. The comparison of results with standard strains underlined good production rates. For C2 and C8 strains, PHA accumulation rates under starvation were higher than Azospirillum brasilense and similar to Synechocystis cf. salina 192. This study broadened the knowledge of the microbial communities of mats and biofilms on the lightened walls of the caves. These findings suggested that these structures, which are common in tourist caves, could be used to isolate valuable strains before remediation measures are adopted.
Impacts of urea and 3,4-dimethylpyrazole phosphate on nitrification, targeted ammonia oxidizers, non-targeted nitrite oxidizers, and bacteria in two contrasting soils
Authors: Wang Qing , Zhao Ziting , Yuan Manyao , Zhang Zhijun , Chen Shanshuai , Ruan Yunze , Huang Qiong
Published: July 2022

This study explored the effects of combined urea and 3,4-dimethylpyrazole phosphate (DMPP) on several components critical to the soil system: net nitrification rates; communities of targeted ammonia oxidizers [ammonia-oxidizing archaea (AOA) and bacteria (AOB) and complete ammonia-oxidizing bacteria (comammox)]; non-targeted nitrite-oxidizing bacteria (NOB) and bacteria. We conducted the study in two contrasting soils (acidic and neutral) over the course of 28 days. Our results indicated that DMPP had higher inhibitory efficacy in the acidic soil (30.7%) compared to the neutral soil (12.1%). The abundance of AOB and Nitrospira-like NOB were positively associated with nitrate content in acidic soil. In neutral soil, these communities were joined by the abundance of AOA and Nitrobacter-like NOB in being positively associated with nitrate content. By blocking the growth of AOB in acidic soil—and the growth of both AOB and comammox in neutral soil—DMPP supported higher rates of AOA growth. Amplicon sequencing of the 16S rRNA gene revealed that urea and urea + DMPP treatments significantly increased the diversity indices of bacteria, including Chao 1, ACE, Shannon, and Simpson in the acidic soil but did not do so in the neutral soil. However, both urea and urea + DMPP treatments obviously altered the community structure of bacteria in both soils relative to the control treatment. This experiment comprehensively analyzed the effects of urea and nitrification inhibitor on functional guilds involved in the nitrification process and non-targeted bacteria, not just focus on targeted ammonia oxidizers.
Bacterial and fungal communities in indoor aerosols from two Kuwaiti hospitals
Authors: Habibi Nazima , Uddin Saif , Behbehani Montaha , Al Salameen Fadila , Razzack Nasreem Abdul , Zakir Farhana , Shajan Anisha , Alam Faiz
Published: July 2022

The airborne transmission of COVID-19 has drawn immense attention to bioaerosols. The topic is highly relevant in the indoor hospital environment where vulnerable patients are treated and healthcare workers are exposed to various pathogenic and non-pathogenic microbes. Knowledge of the microbial communities in such settings will enable precautionary measures to prevent any hospital-mediated outbreak and better assess occupational exposure of the healthcare workers. This study presents a baseline of the bacterial and fungal population of two major hospitals in Kuwait dealing with COVID patients, and in a non-hospital setting through targeted amplicon sequencing. The predominant bacteria of bioaerosols were Variovorax (9.44%), Parvibaculum (8.27%), Pseudonocardia (8.04%), Taonella (5.74%), Arthrospira (4.58%), Comamonas (3.84%), Methylibium (3.13%), Sphingobium (4.46%), Zoogloea (2.20%), and Sphingopyxis (2.56%). ESKAPEE pathogens, such as Pseudomonas, Acinetobacter, Staphylococcus, Enterococcus, and Escherichia, were also found in lower abundances. The fungi were represented by Wilcoxinia rehmii (64.38%), Aspergillus ruber (9.11%), Penicillium desertorum (3.89%), Leptobacillium leptobactrum (3.20%), Humicola grisea (2.99%), Ganoderma sichuanense (1.42%), Malassezia restricta (0.74%), Heterophoma sylvatica (0.49%), Fusarium proliferatum (0.46%), and Saccharomyces cerevisiae (0.23%). Some common and unique operational taxonomic units (OTUs) of bacteria and fungi were also recorded at each site; this inter-site variability shows that exhaled air can be a source of this variation. The alpha-diversity indices suggested variance in species richness and abundance in hospitals than in non-hospital sites. The community structure of bacteria varied spatially (ANOSIM r2 = 0.181–0.243; p < 0.05) between the hospital and non-hospital sites, whereas fungi were more or less homogenous. Key taxa specific to the hospitals were Defluvicoccales, fungi, Ganodermataceae, Heterophoma, and H. sylvatica compared to Actinobacteria, Leptobacillium, L. leptobacillium, and Cordycipitaceae at the non-hospital site (LefSe, FDR q ≤ 0.05). The hospital/non-hospital MD index > 1 indicated shifts in the microbial communities of indoor air in hospitals. These findings highlight the need for regular surveillance of indoor hospital environments to prevent future outbreaks.
High prevalence of spotted fever group rickettsiae in ticks collected from yaks (Bos grunniens) in Shiqu county, eastern Tibetan Plateau, China
Authors: Lin Baoshan , Ta Yin , Hao Lili
Published: July 2022

Tick-borne diseases have become a global health concern in recent decades. Spotted fever group (SFG) rickettsiae have been recognized as important pathogens of human tick-borne diseases worldwide. In this study, Dermacentor everestianus (n = 646) and Haemaphysalis qinghaiensis (n = 172) ticks were collected from yaks (Bos grunniens) in Shiqu county, eastern Tibetan Plateau, China. SFG rickettsiae were identified and characterized in these ticks. A total of 49.9% (408/818) ticks were infected by Rickettsia spp. with infection rates of 58.1% (100/172) and 46.7% (308/646) detected in H. qinghaiensis and D. everestianus ticks, respectively. Furthermore, 95% of Rickettsia spp. were Rickettsia raoultii-like bacteria, and 5% were related to Candidatus Rickettsia longicornii. To the best of our knowledge, this is the first time that SFG rickettsiae infections were firstly reported in Shiqu county for these tick species. Our results indicated that H. qinghaiensis and D. everestianus ticks from Shiqu county became highly infected with a R. raoultii-like bacteria during their feeding process. This observation is alarming because of the zoonotic potentiality of these species. Overall, the present study detected a widespread of R. raoultii-like bacteria in ticks that are considered a serious threat to domestic animals and humans in Shiqu county. The prevalence of R. raoultii-like bacteria in human and wildlife hosts should be further investigated in the future.
Development and evaluation of a multiplex droplet digital polymerase chain reaction method for simultaneous detection of five biothreat pathogens
Authors: Du Yipu , Yan Ziheng , Song Kai , Jin Junyan , Xiao Liting , Sun Zhulin , Tan Yafang , Zhang Pingping , Du Zongmin , Yang Ruifu , Zhao Yong , Song Yajun
Published: July 2022

Biothreat agents pose a huge threat to human and public health, necessitating the development of rapid and highly sensitive detection approaches. This study establishes a multiplex droplet digital polymerase chain reaction (ddPCR) method for simultaneously detecting five high-risk bacterial biothreats: Yersinia pestis, Bacillus anthracis, Brucella spp., Burkholderia pseudomallei, and Francisella tularensis. Unlike conventional multiplex real-time PCR (qPCR) methods, the multiplex ddPCR assay was developed using two types of probe fluorophores, allowing the assay to perform with a common two-color ddPCR system. After optimization, the assay performance was evaluated, showing a lower limit of detection (LOD) (0.1–1.0 pg/μL) and good selectivity for the five bacteria targets. The multiplex assay’s ability to simultaneously detect two or more kinds of targets in a sample was also demonstrated. The assay showed strong sample tolerance when testing simulated soil samples; the LOD for bacteria in soil was 2 × 102–2 × 103 colony-forming unit (CFU)/100 mg soil (around 5–50 CFU/reaction), which was 10-fold lower than that of the single-target qPCR method. When testing simulated soil samples at bacterial concentrations of 2 × 103–2 × 104 CFU/100 mg soil, the assay presented a higher sensitivity (100%, 35/35) than that of the qPCR method (65.71%, 23/35) and a good specificity (100%, 15/15). These results suggest that the developed 5-plex ddPCR method is more sensitive than conventional qPCR methods and is potentially suitable for rapidly detecting or screening the five selected bacterial biothreats in suspicious samples.
Transplantation of fecal microbiota from APP/PS1 mice and Alzheimer’s disease patients enhanced endoplasmic reticulum stress in the cerebral cortex of wild-type mice
Authors: Wang Fang , Gu Yongzhe , Xu Chenhaoyi , Du Kangshuai , Zhao Chence , Zhao Yanxin , Liu Xueyuan
Published: July 2022

Background and purpose

The gut-brain axis is bidirectional and the imbalance of the gut microbiota usually coexists with brain diseases, including Alzheimer’s disease (AD). Accumulating evidence indicates that endoplasmic reticulum (ER) stress is a core lesion in AD and persistent ER stress promotes AD pathology and impairs cognition. However, whether the imbalance of the gut microbiota is involved in triggering the ER stress in the brain remains unknown.

Materials and methods

In the present study, fecal microbiota transplantation (FMT) was performed with gut microbiota from AD patients and APP/PS1 mice, respectively, resulting in two mouse models with dysregulated gut microbiota. The ER stress marker protein levels in the cerebral cortex were assessed using western blotting. The composition of the gut microbiota was assessed using 16S rRNA sequencing.

Results

Excessive ER stress was induced in the cerebral cortex of mice after FMT. Elevated ER stress marker proteins (p-perk/perk, p-eIF2α/eIF2α) were observed, which were rescued by 3,3-dimethyl-1-butanol (DMB). Notably, DMB is a compound that significantly attenuates serum trimethylamine-N-oxide (TMAO), a metabolite of the gut microbiota widely reported to affect cognition.

Conclusion

The findings indicate that imbalance of the gut microbiota induces ER stress in the cerebral cortex, which may be mediated by TMAO.
Dynamic modeling of practice effects across the healthy aging-Alzheimer’s disease continuum
Authors: Bender Andrew R. , Ganguli Arkaprabha , Meiring Melinda , Hampstead Benjamin M. , Driver Charles C.
Published: July 2022

Standardized tests of learning and memory are sensitive to changes associated with both aging and superimposed neurodegenerative diseases. Unfortunately, repeated behavioral test administration can be confounded by practice effects (PE), which may obscure declines in level of abilities and contribute to misdiagnoses. Growing evidence, however, suggests PE over successive longitudinal measurements may differentially predict cognitive status and risk for progressive decline associated with aging, mild cognitive impairment (MCI), and dementia. Thus, when viewed as a reflection of neurocognitive plasticity, PE may reveal residual abilities that can add to our understanding of age- and disease-related changes in learning and memory. The present study sought to evaluate differences in PE and verbal recall in a clinically characterized aging cohort assessed on multiple occasions over 3 years. Participants included 256 older adults recently diagnosed as cognitively unimpaired (CU; n = 126), or with MCI of amnestic (n = 65) or non-amnestic MCI (n = 2085), and multi-domain amnestic dementia of the Alzheimer’s type (DAT; n = 45). We applied a continuous time structural equation modeling (ctsem) approach to verbal recall performance on the Hopkins Verbal Learning Test in order to distinguish PE from individual occasion performance, coupled random changes, age trends, and differing measurement quality. Diagnoses of MCI and dementia were associated with lower recall performance on all trials, reduced PE gain per occasion, and differences in non-linear dynamic parameters. Practice self-feedback is a dynamic measure of the decay or acceleration in PE process changes over longitudinal occasions. As with PE and mean recall, estimated practice self-feedback followed a gradient from positive in CU participants to null in participants with diagnosed MCI and negative for those with dementia diagnoses. Evaluation of sensitivity models showed this pattern of variation in PE was largely unmodified by differences in age, sex, or educational attainment. These results show dynamic modeling of PE from longitudinal performance on standardized learning and memory tests can capture multiple aspects of behavioral changes in MCI and dementia. The present study provides a new perspective for modeling longitudinal change in verbal learning in clinical and cognitive aging research.
Dietary Supplementation With Tinospora cordifolia Improves Anxiety-Type Behavior and Cognitive Impairments in Middle-Aged Acyclic Female Rats
Authors: Bhandari Anmol , Sunkaria Aditya , Kaur Gurcharan
Published: July 2022

The midlife transition period in women marks the progressive flattening of neurological health along with increased adiposity, dyslipidemia, frailty, and inflammatory responses mainly attributed to the gradual decline in estrogen levels. Conflicting reports of hormone replacement therapy (HRT) necessitate the exploration of novel therapeutic interventions using bioactive natural products having the least toxicity and a holistic mode of action for the preservation of metabolic homeodynamics with aging in women. The present study was planned to investigate the effects of aging and/or a high-fat diet (HFD) on cognitive impairments and anxiety and further their management by dietary supplement with the Tinospora cordifolia stem powder (TCP). Acyclic female rats were included in this study as the model system of the perimenopause phase of women along with young 3–4 months old rats as controls. Rats were fed on with and without TCP supplemented normal chow or HFD for 12 weeks. Animals fed on a TCP supplemented normal chow showed consistent management of body weight over a 12-week regimen although their calorie intake was much higher in comparison to their age-matched controls. Post-regimen, neurobehavioral tests, such as novel object recognition and elevated plus maze, performed on these animals showed improvement in their learning and memory abilities as well as the anxiety-like behavior. Furthermore, due to the presence of multiple components, TCP was observed to modulate the expression of key marker proteins to ameliorate neuroinflammation and apoptosis and promote cell survival and synaptic plasticity in the hippocampus and the prefrontal cortex (PFC) regions of the brain. These findings suggest that TCP supplementation in diet during the midlife transition period in women may be a potential interventional strategy for the management of menopause-associated anxiety and cognitive impairments and healthy aging.
The role of Cdk5 in neurological disorders
Authors: Ao Chuncao , Li Chenchen , Chen Jinlun , Tan Jieqiong , Zeng Liuwang
Published: July 2022

Neurological disorders are a group of disorders with motor, sensory or cognitive damage, caused by dysfunction of the central or peripheral nervous system. Cyclin-dependent kinases 5 (Cdk5) is of vital significance for the development of the nervous system, including the migration and differentiation of neurons, the formation of synapses, and axon regeneration. However, when the nervous system is subject to pathological stimulation, aberrant activation of Cdk5 will induce abnormal phosphorylation of a variety of substrates, resulting in a cascade signaling pathway, and thus lead to pathological changes. Cdk5 is intimately related to the pathological mechanism of a variety of neurological disorders, such as A-β protein formation in Alzheimer’s disease, mitochondrial fragmentation in cerebral ischemia, and apoptosis of dopaminergic neurons in Parkinson’s disease. It is worth noting that Cdk5 inhibitors have been reported to have neuroprotective effects by inhibiting related pathological processes. Therefore, in this review, we will briefly introduce the physiological and pathological mechanisms of Cdk5 in the nervous system, focusing on the recent advances of Cdk5 in neurological disorders and the prospect of targeted Cdk5 for the treatment of neurological disorders.
Quantitative EEG parameters can improve the predictive value of the non-traumatic neurological ICU patient prognosis through the machine learning method
Authors: Tian Jia , Zhou Yi , Liu Hu , Qu Zhenzhen , Zhang Limiao , Liu Lidou
Published: July 2022

Background

Better outcome prediction could assist in reliable classification of the illnesses in neurological intensive care unit (ICU) severity to support clinical decision-making. We developed a multifactorial model including quantitative electroencephalography (QEEG) parameters for outcome prediction of patients in neurological ICU.

Methods

We retrospectively analyzed neurological ICU patients from November 2018 to November 2021. We used 3-month mortality as the outcome. Prediction models were created using a linear discriminant analysis (LDA) based on QEEG parameters, APACHEII score, and clinically relevant features. Additionally, we compared our best models with APACHEII score and Glasgow Coma Scale (GCS). The DeLong test was carried out to compare the ROC curves in different models.

Results

A total of 110 patients were included and divided into a training set (n=80) and a validation set (n = 30). The best performing model had an AUC of 0.85 in the training set and an AUC of 0.82 in the validation set, which were better than that of GCS (training set 0.64, validation set 0.61). Models in which we selected only the 4 best QEEG parameters had an AUC of 0.77 in the training set and an AUC of 0.71 in the validation set, which were similar to that of APACHEII (training set 0.75, validation set 0.73). The models also identified the relative importance of each feature.

Conclusion

Multifactorial machine learning models using QEEG parameters, clinical data, and APACHEII score have a better potential to predict 3-month mortality in non-traumatic patients in neurological ICU.
Alterations in motor modules and their contribution to limitations in force control in the upper extremity after stroke
Authors: Seo Gang , Lee Sang Wook , Beer Randall F. , Alamri Amani , Wu Yi-Ning , Raghavan Preeti , Rymer William Z. , Roh Jinsook
Published: July 2022

The generation of isometric force at the hand can be mediated by activating a few motor modules. Stroke induces alterations in motor modules underlying steady-state isometric force generation in the human upper extremity (UE). However, how the altered motor modules impact task performance (force production) remains unclear as stroke survivors develop and converge to the three-dimensional (3D) target force. Thus, we tested whether stroke-specific motor modules would be activated from the onset of force generation and also examined how alterations in motor modules would induce changes in force representation. During 3D isometric force development, electromyographic (EMG) signals were recorded from eight major elbow and shoulder muscles in the paretic arm of 10 chronic hemispheric stroke survivors and both arms of six age-matched control participants. A non-negative matrix factorization algorithm identified motor modules in four different time windows: three “exploratory” force ramping phases (Ramps 1–3; 0–33%, 33–67%, and 67–100% of target force magnitude, respectively) and the stable force match phase (Hold). Motor module similarity and between-force coupling were examined by calculating the scalar product and Pearson correlation across the phases. To investigate the association between the end-point force representation and the activation of the motor modules, principal component analysis (PCA) and multivariate multiple linear regression analyses were applied. In addition, the force components regressed on the activation profiles of motor modules were utilized to model the feasible force direction. Both stroke and control groups developed exploratory isometric forces with a non-linear relationship between EMG and force. During the force matching, only the stroke group showed abnormal between-force coupling in medial-lateral and backward-forward and medial-lateral and downward-upward directions. In each group, the same motor modules, including the abnormal deltoid module in stroke survivors, were expressed from the beginning of force development instead of emerging during the force exploration. The PCA and the multivariate multiple linear regression analyses showed that alterations in motor modules were associated with abnormal between-force coupling and limited feasible force direction after stroke. Overall, these results suggest that alterations in intermuscular coordination contribute to the abnormal end-point force control under isometric conditions in the UE after stroke.
Microglial re-modeling contributes to recovery from ischemic injury of rat brain: A study using a cytokine mixture containing granulocyte-macrophage colony-stimulating factor and interleukin-3
Authors: Matsumoto Shirabe , Choudhury Mohammed E. , Takeda Haruna , Sato Arisa , Kihara Nanako , Mikami Kanta , Inoue Akihiro , Yano Hajime , Watanabe Hideaki , Kumon Yoshiaki , Kunieda Takeharu , Tanaka Junya
Published: July 2022

Ischemic stroke is a leading cause of mortality and permanent disability. Chronic stroke lesions increase gradually due to the secondary neuroinflammation that occurs following acute ischemic neuronal degeneration. In this study, the ameliorating effect of a cytokine mixture consisting of granulocyte-macrophage colony-stimulating factor (GM-CSF) and interleukin (IL)-3 was evaluated on ischemic brain injury using a rat stroke model prepared by transient middle cerebral artery occlusion (tMCAO). The mixture reduced infarct volume and ameliorated ischemia-induced motor and cognitive dysfunctions. Sorted microglia cells from the ischemic hemisphere of rats administered the mixture showed reduced mRNA expression of tumor necrosis factor (TNF)-α and IL-1β at 3 days post-reperfusion. On flow cytometric analysis, the expression of CD86, a marker of pro-inflammatory type microglia, was suppressed, and the expression of CD163, a marker of tissue-repairing type microglia, was increased by the cytokine treatment. Immunoblotting and immunohistochemistry data showed that the cytokines increased the expression of the anti-apoptotic protein Bcl-xL in neurons in the ischemic lesion. Thus, the present study demonstrated that cytokine treatment markedly suppressed neurodegeneration during the chronic phase in the rat stroke model. The neuroprotective effects may be mediated by phenotypic changes of microglia that presumably lead to increased expression of Bcl-xL in ischemic lesions, while enhancing neuronal survival.
Research in Mindfulness Interventions for Patients With Fibromyalgia: A Critical Review
Authors: Leça Salomé , Tavares Isaura
Published: July 2022

Fibromyalgia is one of the most common causes of widespread chronic pain. It has a huge impact on the quality of life, namely because it appears earlier in life than most of the chronic pain conditions. Furthermore, emotional-cognitive distress factors, such as depression and anxiety, are a common feature in patients with fibromyalgia. The neurobiological mechanisms underlying fibromyalgia remain mostly unknown. Among non-pharmacological treatments, cognitive-behavioral therapy has been used during the last decade, namely with the enrolment of patients in programs of mindfulness-based stress reduction (MBSR) and in mindfulness-based interventions (MBI). We critically analyzed the literature to search for scientific evidence for the use of MBI in fibromyalgia. The studies were evaluated as to several outcomes of fibromyalgia improvement along with aspects of the study design which are currently considered relevant for research in mindfulness. We conclude that despite the sparsity of well-structured longitudinal studies, there are some promising results showing that the MBI are effective in reducing the negative aspects of the disease. Future design of studies using MBI in fibromyalgia management should be critically discussed. The importance of active controls, evaluation of sustained effects along with investigation of the subserving neurobiological mechanisms and detailed reports of possible adverse effects should be considered.