bluuebunny/crossref_metadata_2025 huggingface dataset:
Vascular Abnormalities in Peripapillary and Macular Regions of Behcet's Uveitis Patients Evaluated by Optical Coherence Tomography Angiography
Authors: Yan Chun , Li Fan , Hou Min , Ye Xiaoyuan , Su Lishi , Hu Yixin , Luo Jiawen , Chi Wei
Published: September 2021

Purpose: To investigate the involvement of peripapillary zone vascular abnormalities in Behcet's uveitis (BU) and associated visual dysfunction. We evaluated the retinal and choroidal microvascular features in both macular and peripapillary areas of BU patients to identify vascular abnormalities contributing to reduced best-corrected visual acuity (BCVA) using optical coherence tomography angiography (OCTA).

Methods: A prospective, observational study was conducted in 24 eyes of 13 patients with BU and 24 eyes of 15 healthy participants as controls. They received a standard eye examination and were recorded by OCTA measurements of macular and peripapillary areas. The vascular densities of superficial capillary plexus (SCP) and deep capillary plexus (DCP), choroidal flow area, radial peripapillary capillary network (RPCN) density, foveal avascular zone (FAZ) area and perimeter, full retinal thickness (FRT), and peripapillary retinal nerve fiber layer thickness (pRNFLT) were measured.Correlations among microvascular, structural, and functional changes were assessed.

Results: Our findings uncovered that the vascular density was significantly reduced in the peripapillary zone of BU eyes compared to healthy eyes, especially in the inferior subfield of the RPCN. The vascular densities of SCP and DCP quadrants within the macular zone had no significant difference between BU and control groups except for DCP density of the nasal parafoveal quadrant. Both FAZ area and perimeter were greater but without statistical significance in the BU group. Compared to healthy eyes, the choriocapillaris flow area was smaller while the FRT and pRNFLT were greater in the BU group. Notably, there was a significant correlation between the reduction in RPCN vascular density and decreased BCVA in BU patients.

Conclusion: Based on OCTA, vascular changes associated with BU are more prominent in the peripapillary zone than those in the macular zone. The vascular density of the RPCN could serve as a sensitive indicator to monitoring BU pathogenic progression and treatment response using a non-invasively method of OCTA.
Elaboration of a Radiomics Strategy for the Prediction of the Re-positive Cases in the Discharged Patients With COVID-19
Authors: Wang Xiao-Hui , Xu Xiaopan , Ao Zhi , Duan Jun , Han Xiaoli , Tang Xing , Fu Yu-Fei , Wu Xu-Sha , Wang Xue , Zhu Linxiao , Zeng Wenbing , Guo Shuliang
Published: September 2021

Objective: A considerable part of COVID-19 patients were found to be re-positive in the SARS-CoV-2 RT-PCR test after discharge. Early prediction of re-positive COVID-19 cases is of critical importance in determining the isolation period and developing clinical protocols.

Materials and Methods: Ninety-one patients discharged from Wanzhou Three Gorges Central Hospital, Chongqing, China, from February 10, 2020 to March 3, 2020 were administered nasopharyngeal swab SARS-CoV-2 tests within 12–14 days, and 50 eligible patients (32 male and 18 female) with completed data were enrolled. Average age was 48 ± 11.5 years. All patients underwent non-enhanced chest CT on admission. A total of 568 radiomics features were extracted from the CT images, and 17 clinical factors were collected based on the medical record. Student's t-test and support vector machine–based recursive feature elimination (SVM-RFE) method were used to determine an optimal subset of features for the discriminative model development.

Results: After Student's t-test, 62 radiomics features showed significant inter-group differences (p < 0.05) between the re-positive and negative cases, and none of the clinical features showed significant differences. These significant features were further selected by SVM-RFE algorithm, and a more compact feature subset containing only two radiomics features was finally determined, achieving the best predictive performance with the accuracy and area under the curve of 72.6% and 0.773 for the identification of the re-positive case.

Conclusion: The proposed radiomics method has preliminarily shown potential in identifying the re-positive cases among the recovered COVID-19 patients after discharge. More strategies are to be integrated into the current pipeline to improve its precision, and a larger database with multi-clinical enrollment is required to extensively verify its performance.
Managing Psoriatic Arthritis With Inflammatory Bowel Disease and/or Uveitis
Authors: Chia Alfred Yu Ting , Ang Gladys Wei Xin , Chan Anita Sook Yee , Chan Webber , Chong Timothy Kit Yeong , Leung Ying Ying
Published: September 2021

Psoriatic arthritis (PsA) is a chronic inflammatory disease that presents with psoriasis (PsO), peripheral and axial arthropathy. The heterogeneity of disease presentation leads to the term “psoriatic disease (PsD)” which is thought to better encompass the range of clinical manifestations. PsA is associated with several comorbidities such as cardiovascular diseases, metabolic syndrome and other extra-articular manifestations including uveitis, and inflammatory bowel disease (IBD). While novel therapeutics are being developed following advances in our understanding of the pathogenesis of the disease, the diverse combinations of PsA with its various comorbidities still pose a clinical challenge in managing patients with PsA. This article reviews our current understanding of the pathogenesis of PsA and how various pathways in the pathogenesis lead to the two comorbid extra-articular manifestations – uveitis and IBD. We also review current evidence of treatment strategies in managing patients with PsA with comorbidities of uveitis and/or IBD.
Effects of Clostridium butyricum, Sodium Butyrate, and Butyric Acid Glycerides on the Reproductive Performance, Egg Quality, Intestinal Health, and Offspring Performance of Yellow-Feathered Breeder Hens
Authors: Wang Yibing , Wang Yang , Lin Xiajing , Gou Zhongyong , Fan Qiuli , Jiang Shouqun
Published: September 2021

Butyrate has been reported to promote the performance and growth of chickens. The specific roles and efficacy of different sources of butyrate remained unclear. Thus, the present study aimed to investigate and compare the effects of Clostridium butyricum (CB), sodium butyrate (SB), and butyric acid glycerides (tributyrin, BAG) on the reproductive performance, egg quality, intestinal health, and offspring performance of yellow-feathered breeder hens. A total of 300 Lingnan yellow-feathered breeder hens were assigned to five treatment groups: control (CL), 1×108CFU/kg CB (CBL), 1×109CFU/kg CB (CBH), 500mg/kg SB, and 300mg/kg BAG. Results showed that the laying performance and egg quality were increased by CBL, CBH, and BAG. Both CB treatments increased the hatchability of fertilized eggs. Maternal supplementation with both levels of CB significantly elevated the growth performance of offspring. Treatment with CBL, CBH, SB, and BAG all improved the oviduct-related variables and reduced the plasmal antioxidant variables. The CBH, CBL, and BAG treatments also improved the intestinal morphology to different degrees. Jejunal contents of IL-6 were decreased by CBH and BAG, while those of IL-4, IL-6, IL-1β, and IgY were decreased by SB. Transcripts of nutrient transporters in jejunal mucosa were also upregulated by CBH, CBL, and SB treatments and expression of Bcl-2-associated X protein was decreased by CBL, CBH, and BAG. In cecal contents, CBL increased the abundance of Firmicutes and Bacillus, while CBH decreased the abundance of Proteobacteria. Also, the co-occurrence networks of intestinal microbes were regulated by CBH and BAG. In conclusion, dietary inclusion of CB and BAG improved the reproductive parameters, egg quality, and intestinal morphology of breeders. CB also influenced the hatching performance of breeders and growth performance of the offspring, while SB improved the oviduct-related variables. These beneficial effects may result from the regulation of cytokines, nutrient transporters, apoptosis, and gut microbiota; high-level CB had more obvious impact. Further study is needed to explore and understand the correlation between the altered gut microbiota induced by butyrate and the performance, egg quality, intestinal health, and also offspring performance.
Serotyping, MLST, and Core Genome MLST Analysis of Salmonella enterica From Different Sources in China During 2004–2019
Authors: Yan Shigan , Zhang Wencheng , Li Chengyu , Liu Xu , Zhu Liping , Chen Leilei , Yang Baowei
Published: September 2021

Salmonella enterica (S. enterica) is an important foodborne pathogen, causing food poisoning and human infection, and critically threatening food safety and public health. Salmonella typing is essential for bacterial identification, tracing, epidemiological investigation, and monitoring. Serotyping and multilocus sequence typing (MLST) analysis are standard bacterial typing methods despite the low resolution. Core genome MLST (cgMLST) is a high-resolution molecular typing method based on whole genomic sequencing for accurate bacterial tracing. We investigated 250 S. enterica isolates from poultry, livestock, food, and human sources in nine provinces of China from 2004 to 2019 using serotyping, MLST, and cgMLST analysis. All S. enterica isolates were divided into 36 serovars using slide agglutination. The major serovars in order were Enteritidis (31 isolates), Typhimurium (29 isolates), Mbandaka (23 isolates), and Indiana (22 isolates). All strains were assigned into 43 sequence types (STs) by MLST. Among them, ST11 (31 isolates) was the primary ST. Besides this, a novel ST, ST8016, was identified, and it was different from ST40 by position 317 C → T in dnaN. Furthermore, these 250 isolates were grouped into 185 cgMLST sequence types (cgSTs) by cgMLST. The major cgST was cgST235530 (11 isolates), and only three cgSTs contained isolates from human and other sources, indicating a possibility of cross-species infection. Phylogenetic analysis indicated that most of the same serovar strains were putatively homologous except Saintpaul and Derby due to their multilineage characteristics. In addition, serovar I 4,[5],12:i:- and Typhimurium isolates have similar genomic relatedness on the phylogenetic tree. In conclusion, we sorted out the phenotyping and genotyping diversity of S. enterica isolates in China during 2004–2019 and clarified the temporal and spatial distribution characteristics of Salmonella from different hosts in China in the recent 16 years. These results greatly supplement Salmonella strain resources, genetic information, and traceability typing data; facilitate the typing, traceability, identification, and genetic evolution analysis of Salmonella; and therefore, improve the level of analysis, monitoring, and controlling of foodborne microorganisms in China.
Comparative Metagenomics Reveals Microbial Communities and Their Associated Functions in Two Types of Fuzhuan Brick Tea
Authors: Wang Xin , Du Gengan , Chen Hong , Zeng Xuejun , Liu Bin , Guo Chunfeng , Sheng Qinglin , Yuan Yahong , Yue Tianli
Published: September 2021

Fuzhuan brick tea (FBT) is a unique post-fermented tea product, naturally co-fermented by microorganisms, and has gained global popularity due to its potential health benefits for humans. Considerable efforts have been made toward elucidating the microbial diversity within FBT, but an understanding of the underlying FBT community interactions and functions remains poorly studied. Consequently, the microbial communities of two types of FBT, originating from Hunan and Shaanxi provinces, were investigated using comparative shotgun metagenomic sequencing and functional annotations. Metagenomic analysis indicated that two communities shared similar taxonomic and functional attributes. Two samples shared 486 genera, in which Pseudomonas contributed most to the abundant functions within the two samples. The carbohydrate active enzyme functions of the communities primarily comprised GH (32.92%), GT (26.8%), CEs (20.43%), and AAs (18.04%). Furthermore, the overall metabolic pathways encoded by the metagenomes were largely associated with carbohydrate and amino acid metabolism, with nine metabolic pathways that were differential between two groups including penicillin and cephalosporin biosynthesis. Significantly, a total of 35 potential probiotics were inferred, with Pseudomonas putida being the most abundant inferred probiotic (80%) within the FBT communities. This study provides new insights into FBT microbial communities on their potential functions and roles in FBT characteristics.
Establishment of Tree Shrew Animal Model for Kaposi’s Sarcoma-Associated Herpesvirus (HHV-8) Infection
Authors: Li Daoqun , Baloch Zulqarnain , Zhao Yang , Bai Lei , Wang Xing , Wang Gang , Zhang A-Mei , Lan Ke , Xia Xueshan
Published: September 2021

Kaposi’s sarcoma-associated herpesvirus (KSHV) is the most common cause of Kaposi’s sarcoma (KS) and other malignant growths in humans. However, the lack of a KSHV-infected small animal model has hampered understanding of the mechanisms of KSHV infection, virus replication, pathogenesis, and persistence. This study was designed to explore the susceptibility of tree shrews as a possible KSHV-infected small animal model. A recombinant GFP (latent)/RFP (lytic)-positive rKSHV.219 strain was used to infect primary cells cultured from different tissues of tree shrews as an in vitro model and adult tree shrews as an in vivo model. KSHV latent nuclear antigen (LANA) and DNA were successfully detected in primary cells of tree shrews. Among them, tree shrew kidney epithelial cells (TSKEC) were the most susceptible cells to KSHV infection compared to other cells. KSHV genomic DNA, mRNA, and KSHV-specific proteins were readily detected in the TSKEC cultured up to 32 dpi. Moreover, KSHV DNA and mRNA transcription were also readily detected in the peripheral blood mononuclear cells (PBMCs) and various tissues of tree shrews infected with KSHV. Haematoxylin and eosin (HE) staining showed lymphocyte infiltration, lymphoid tissue focal aggregation, alveolar wall thickening, hepatocyte edema, hepatic necrosis in the spleen, lung, and liver of KSHV-infected animals. Additionally, immune-histochemical (IHC) staining showed that LANA or ORF62-positive cells were present in the spleen, lung, liver, and kidney of KSHV-infected tree shrews. Here, we have successfully established in vitro and in vivo KSHV latent infection in tree shrews. This small animal model is not only useful for studying the pathogenesis of KSHV in vivo but can also be a useful model to study transmission routes of viral infection and a useful platform to characterize the novel therapeutics against KSHV.
Performance Evaluation of the Gradient Diffusion Strip Method and Disk Diffusion Method for Ceftazidime–Avibactam Against Enterobacterales and Pseudomonas aeruginosa: A Dual-Center Study
Authors: Zhang Jingjia , Li Gang , Zhang Ge , Kang Wei , Duan Simeng , Wang Tong , Li Jin , Huangfu Zhiru , Yang Qiwen , Xu Yingchun , Jia Wei , Sun Hongli
Published: September 2021

Objectives: Ceftazidime–avibactam is a novel synthetic beta-lactam + beta-lactamase inhibitor combination. We evaluated the performance of the gradient diffusion strip method and the disk diffusion method for the determination of ceftazidime–avibactam against Enterobacterales and Pseudomonas aeruginosa.

Methods: Antimicrobial susceptibility testing of 302 clinical Enterobacterales and Pseudomonas aeruginosa isolates from two centers were conducted by broth microdilution (BMD), gradient diffusion strip method, and disk diffusion method for ceftazidime–avibactam. Using BMD as a gold standard, essential agreement (EA), categorical agreement (CA), major error (ME), and very major error (VME) were determined according to CLSI guidelines. CA and EA rate > 90%, ME rate < 3%, and VME rate < 1.5% were considered as acceptable criteria. Polymerase chain reaction and Sanger sequencing were performed to determine the carbapenem resistance genes of all 302 isolates.

Results: A total of 302 strains were enrolled, among which 182 strains were from center 1 and 120 strains were from center 2. A percentage of 18.21% (55/302) of the enrolled isolates were resistant to ceftazidime–avibactam. The CA rates of the gradient diffusion strip method for Enterobacterales and P. aeruginosa were 100% and 98.65% (73/74), respectively, and the EA rates were 97.37% (222/228) and 98.65% (73/74), respectively. The CA rates of the disk diffusion method for Enterobacterales and P. aeruginosa were 100% and 95.95% (71/74), respectively. No VMEs were found by using the gradient diffusion strip method, while the ME rate was 0.40% (1/247). No MEs were found by using the disk diffusion method, but the VME rate was 5.45% (3/55). Therefore, all the parameters of the gradient diffusion strip method were in line with acceptable criteria. For 31 blaKPC, 33 blaNDM, 7 blaIMP, and 2 blaVIM positive isolates, both CA and EA rates were 100%; no MEs or VMEs were detected by either method. For 15 carbapenemase-non-producing resistant isolates, the CA and EA rates of the gradient diffusion strips method were 100%. Whereas the CA rate of the disk diffusion method was 80.00% (12/15), the VME rate was 20.00% (3/15).

Conclusion: The gradient diffusion strip method can meet the needs of clinical microbiological laboratories for testing the susceptibility of ceftazidime–avibactam drugs. However, the VME rate > 1.5% (5.45%) by the disk diffusion method. By comparison, the performance of the gradient diffusion strip method was better than that of the disk diffusion method.
Effect of Methane Inhibitors on Ruminal Microbiota During Early Life and Its Relationship With Ruminal Metabolism and Growth in Calves
Authors: Cristobal-Carballo Omar , McCoard Susan A. , Cookson Adrian L. , Ganesh Siva , Lowe Katherine , Laven Richard A. , Muetzel Stefan
Published: September 2021

The present study aimed to determine whether dietary supplementation with methanogen inhibitors during early life may lead to an imprint on the rumen microbial community and change the rumen function and performance of calves to 49-weeks of rearing. Twenty-four 4-day-old Friesian x Jersey cross calves were randomly assigned into a control and a treatment group. Treated calves were fed a combination of chloroform (CF) and 9,10-anthraquinone (AQ) in the solid diets during the first 12 weeks of rearing. Afterward, calves were grouped by treatments until week 14, and then managed as a single group on pasture. Solid diets and water were offeredad libitum. Methane measurements, and sample collections for rumen metabolite and microbial community composition were carried out at the end of weeks 2, 4, 6, 8, 10, 14, 24 and 49. Animal growth and dry matter intake (DMI) were regularly monitored over the duration of the experiment. Methane emissions decreased up to 90% whilst hydrogen emissions increased in treated compared to control calves, but only for up to 2 weeks after treatment cessation. The near complete methane inhibition did not affect calves’ DMI and growth. The acetate:propionate ratio decreased in treated compared to control calves during the first 14 weeks but was similar at weeks 24 and 49. The proportions ofMethanobrevibacterandMethanosphaeradecreased in treated compared to control calves during the first 14 weeks; however, at week 24 and 49 the archaea community was similar between groups. Bacterial proportions at the phylum level and the abundant bacterial genera were similar between treatment groups. In summary, methane inhibition increased hydrogen emissions, altered the methanogen community and changed the rumen metabolite profile without major effects on the bacterial community composition. This indicated that the main response of the bacterial community was not a change in composition but rather a change in metabolic pathways. Furthermore, once methane inhibition ceased the methanogen community, rumen metabolites and hydrogen emissions became similar between treatment groups, indicating that perhaps using the treatments tested in this study, it is not possible to imprint a low methane microbiota into the rumen in the solid feed of pre-weaned calves.
Bacillus subtilis DSM29784 Alleviates Negative Effects on Growth Performance in Broilers by Improving the Intestinal Health Under Necrotic Enteritis Challenge
Authors: Wang Yuanyuan , Xu Yibin , Xu Shengliang , Yang Jinyong , Wang Kaiying , Zhan Xiuan
Published: September 2021

Along with banning antibiotics, necrotic enteritis (NE), especially subclinical enteritis (SNE), poses a significant threat to the chicken industry; however, probiotics are a potentially promising intervention. We aimed to investigate the beneficial effects of Bacillus subtilis DSM29784 (BS) on the treatment of Clostridium perfringens (CP)-induced SNE in broilers. A total of 360 1-day-old broiler chicks were divided into three treatment groups, namely control (Ctr), SNE, and BS treatment (BST) groups, all of which were fed with a basal died for 21days, and then from day 22 onward, only the BST group had a BS supplemented diet (1×109 colony-forming units BS/kg). On day 15, all chicks, except the Ctr group, were challenged with a 20-fold dose coccidiosis vaccine and 1ml CP (2×108) on days 18–21 for SNE induction. Beneficial effects were observed on growth performance in BST compared to SNE broilers. BST treatment alleviated intestinal lesions and increased the villus height/crypt depth ratio. Further, BST broilers showed increased maltase activity in the duodenum compared with SNE chicks, and a significantly decreased caspase-3 protein expression in the jejunum mucosa. Moreover, an increased abundance of Ruminococcaceae and Bifidobacterium beneficial gut bacteria and an altered gut metabolome were observed. Taken together, we demonstrate that the manipulation of microbial gut composition using probiotics may be a promising prevention strategy for SNE by improving the composition and metabolism of the intestinal microbiota, intestinal structure, and reducing inflammation and apoptosis. Hence, BS potentially has active ingredients that may be used as antibiotic substitutes and effectively reduces the economic losses caused by SNE. The findings of this study provide a scientific foundation for BS application in broiler feed in the future.
Genome of Ganoderma Species Provides Insights Into the Evolution, Conifers Substrate Utilization, and Terpene Synthesis for Ganoderma tsugae
Authors: Jiang Nan , Hu Shuang , Peng Bing , Li Zhenhao , Yuan Xiaohui , Xiao Shijun , Fu Yongping
Published: September 2021

Ganoderma tsugae is an endemic medicinal mushroom in Northeast China, providing important source of pharmaceutical product. Comparing with other Ganoderma species, wild G. tsugae can utilize coniferous wood. However, functional genes related to medicinal component synthesis and the genetic mechanism of conifer substrate utilization is still obscure. Here, we assembled a high-quality G. tsugae genome with 18 contigs and 98.5% BUSCO genes and performed the comparative genomics with other Ganoderma species. G. tsugae diverged from their common ancestor of G. lingzhi and G. sinense about 21 million years ago. Genes in G. tsugae-specific and G. tsugae-expanded gene families, such as salh, phea, cyp53a1, and cyp102a, and positively selected genes, such as glpk and amie, were functionally enriched in plant-pathogen interaction, benzoate degradation, and fanconi anemia pathway. Those functional genes might contribute to conifer substrate utilization of G. tsugae. Meanwhile, gene families in the terpene synthesis were identified and genome-wide SNP variants were detected in population. Finally, the study provided valuable genomic resources and offered useful hints for the functional gene mapping and investigation of key gene contributing to conifer cultivation substrate utilization and medicinal component biosynthesis.
Transcriptomic Analysis of Pediococcus pentosaceus Reveals Carbohydrate Metabolic Dynamics Under Lactic Acid Stress
Authors: Han Dong , Yan Qiaojuan , Liu Jun , Jiang Zhengqiang , Yang Shaoqing
Published: September 2021

Stress physiology of lactic acid bacteria (LAB) is crucial to their ecological fitness and applicational implications. As a self-imposed stress, lactic acid is the major final metabolic product of LAB and its accumulation can be detrimental to bacterial cells. However, the relationship between LAB carbohydrate metabolism, the primary energy supplying bioactivities, and lactic acid stress responses is not fully understood. Pediococcus pentosaceus has been recognized as an important cell factory and demonstrated probiotic activities. This study investigated behavior of P. pentosaceus under lactic and acetic acid stresses, particularly with supplementations of metabolizable carbohydrates. Lactic and acetic acid retain similar growth stagnation effect, and both resulted in cell death in P. pentosaceus. All metabolizable carbohydrates improved bacterial survival compared to lactic acid control, while xylooligosaccharides (XOS) exerted the highest viability protective efficacy, 0.82 log CFU/mL higher population survived than other carbohydrates after 30 h of incubation. RNA-seq pipeline showcased the intensive global transcriptional responses of P. pentosaceus to lactic acid, which caused significant regulations (more than 2 Log2 fold) of 16.5% of total mRNA coding genes. Glucose mainly led to gene suppressions (83 genes) while XOS led to gene up-regulations (19 genes) under lactic acid stress. RT-qPCR study found that RNA polymerase-centered transcriptional regulation is the primary regulatory approach in evaluated culture conditions. The synergy between lactic acid stress and carbohydrate metabolism should be attentively contemplated in future studies and applications.
Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity
Authors: Birikmen Mehmet , Bohnsack Katherine E. , Tran Vinh , Somayaji Sharvari , Bohnsack Markus T. , Ebersberger Ingo
Published: September 2021

Ribosome assembly is an essential and carefully choreographed cellular process. In eukaryotes, several 100 proteins, distributed across the nucleolus, nucleus, and cytoplasm, co-ordinate the step-wise assembly of four ribosomal RNAs (rRNAs) and approximately 80 ribosomal proteins (RPs) into the mature ribosomal subunits. Due to the inherent complexity of the assembly process, functional studies identifying ribosome biogenesis factors and, more importantly, their precise functions and interplay are confined to a few and very well-established model organisms. Although best characterized in yeast (Saccharomyces cerevisiae), emerging links to disease and the discovery of additional layers of regulation have recently encouraged deeper analysis of the pathway in human cells. In archaea, ribosome biogenesis is less well-understood. However, their simpler sub-cellular structure should allow a less elaborated assembly procedure, potentially providing insights into the functional essentials of ribosome biogenesis that evolved long before the diversification of archaea and eukaryotes. Here, we use a comprehensive phylogenetic profiling setup, integrating targeted ortholog searches with automated scoring of protein domain architecture similarities and an assessment of when search sensitivity becomes limiting, to trace 301 curated eukaryotic ribosome biogenesis factors across 982 taxa spanning the tree of life and including 727 archaea. We show that both factor loss and lineage-specific modifications of factor function modulate ribosome biogenesis, and we highlight that limited sensitivity of the ortholog search can confound evolutionary conclusions. Projecting into the archaeal domain, we find that only few factors are consistently present across the analyzed taxa, and lineage-specific loss is common. While members of the Asgard group are not special with respect to their inventory of ribosome biogenesis factors (RBFs), they unite the highest number of orthologs to eukaryotic RBFs in one taxon. Using large ribosomal subunit maturation as an example, we demonstrate that archaea pursue a simplified version of the corresponding steps in eukaryotes. Much of the complexity of this process evolved on the eukaryotic lineage by the duplication of ribosomal proteins and their subsequent functional diversification into ribosome biogenesis factors. This highlights that studying ribosome biogenesis in archaea provides fundamental information also for understanding the process in eukaryotes.
Multifrequency STD NMR Unveils the Interactions of Antibiotics With Burkholderia multivorans Biofilm Exopolysaccharide
Authors: Nepravishta Ridvan , Monaco Serena , Distefano Marco , Rizzo Roberto , Cescutti Paola , Angulo Jesus
Published: September 2021

Biofilms confine bacterial cells within self-produced matrices, offering advantages such as protection from antibiotics and entrapment of nutrients. Polysaccharides are major components in these macromolecular assemblies, and their interactions with other chemicals are of high relevance for the benefits provided by the biofilm 3D molecular matrix. NMR is a powerful technique for the study and characterization of the interactions between molecules of biological relevance. In this study, we have applied multifrequency saturation transfer difference (STD) NMR and DOSY NMR approaches to elucidate the interactions between the exopolysaccharide produced by Burkholderia multivorans C1576 (EpolC1576) and the antibiotics kanamycin and ceftadizime. The NMR strategies presented here allowed for an extensive characterization at an atomic level of the mechanisms behind the implication of the EpolC1576 in the recalcitrance phenomena, which is the ability of bacteria in biofilms to survive in the presence of antibiotics. Our results suggest an active role for EpolC1576 in the recalcitrance mechanisms toward kanamycin and ceftadizime, though through two different mechanisms.
Gout Is Not Just Arthritis: Abnormal Cortical Thickness and Structural Covariance Networks in Gout
Authors: Yang Yifan , Cheng Yuqi , Wang Xiangyu , Upreti Bibhuti , Cui Ruomei , Liu Shuang , Shan Baoci , Yu Hongjun , Luo Chunrong , Xu Jian
Published: September 2021

Background: Hyperuricemia is the cause of gout. The antioxidant and neuroprotective effects of uric acid seem to benefit some patients with central nervous system injury. However, changes in the brain structure have not been discovered in patients with gout.

Object: Clarify the changes in cortical thickness in patients with gout and the alteration of the structural covariance networks (SCNs) based on cortical thickness.

Methods: We collected structural MRIs of 23 male gout patients and 23 age-matched healthy controls. After calculating and comparing the difference in cortical thickness between the two groups, we constructed and analyzed the cortical thickness covariance networks of the two groups, and we investigated for any changes in SCNs of gout patients.

Results: Gout patients have thicker cortices in the left postcentral, left supramarginal, right medial temporal, and right medial orbitofrontal regions; and thinner cortices were found in the left insula, left superior frontal, right pericalcarine, and right precentral regions. In SCN analysis, between-group differences in global network measures showed that gout patients have a higher global efficiency. In regional network measures, more nodes in gout patients have increased centrality. In network hub analysis, we found that the transfer of the core hub area, rather than the change in number, may be the characteristic of the gout's cortical thickness covariance network.

Conclusion: This is the first study on changes in brain cortical thickness and SCN based on graph theory in patients with gout. The present study found that, compared with healthy controls, gout patients show regional cortical thinning or thickening, and variation in the properties of the cortical thickness covariance network also changed. These alterations may be the combined effect of disease damage and physiological compensation. More research is needed to fully understand the complex underlying mechanisms of gout brain variation.
Spatial Cognition in Children With Physical Disability; What Is the Impact of Restricted Independent Exploration?
Authors: Farran Emily K. , Critten Valerie , Courbois Yannick , Campbell Emma , Messer David
Published: September 2021

Given the developmental inter-relationship between motor ability and spatial skills, we investigated the impact of physical disability (PD) on spatial cognition. Fifty-three children with special educational needs including PD were divided into those who were wheelchair users (n = 34) and those with independent locomotion ability (n = 19). This division additionally enabled us to determine the impact of limited independent physical exploration (i.e., required wheelchair use) on spatial competence. We compared the spatial performance of children in these two PD groups to that of typically developing (TD) children who spanned the range of non-verbal ability of the PD groups. Participants completed three spatial tasks; a mental rotation task, a spatial programming task and a desktop virtual reality (VR) navigation task. Levels of impairment of the PD groups were broadly commensurate with their overall level of non-verbal ability. The exception to this was the performance of the PD wheelchair group on the mental rotation task, which was below that expected for their level of non-verbal ability. Group differences in approach to the spatial programming task were evident in that both PD groups showed a different error pattern from the TD group. These findings suggested that for children with both learning difficulties and PD, the unique developmental impact on spatial ability of having physical disabilities, over and above the impact of any learning difficulties, is minimal.
Frequent, Short Physical Activity Breaks Reduce Prefrontal Cortex Activation but Preserve Working Memory in Middle-Aged Adults: ABBaH Study
Authors: Heiland Emerald G. , Tarassova Olga , Fernström Maria , English Coralie , Ekblom Örjan , Ekblom Maria M.
Published: September 2021

Prolonged sitting is increasingly common and may possibly be unfavorable for cognitive function and mood. In this randomized crossover study, the effects of frequent, short physical activity breaks during prolonged sitting on cognitive task-related activation of the prefrontal cortex were investigated. The effects on working memory, psychological factors, and blood glucose were also examined, and whether arterial stiffness moderated prefrontal cortex activation. Thirteen subjects (mean age 50.5 years; eight men) underwent three 3-h sitting conditions, interrupted every 30-min by a different 3-min break on separate, randomized-ordered days: seated social interactions (SOCIAL), walking (WALK), or simple resistance activities (SRA). Arterial stiffness was assessed at baseline. Before and after each 3-h condition, psychological factors (stress, mood, sleepiness, and alertness) were assessed through questionnaires and functional near-infrared spectroscopy (fNIRS) was used to measure changes in prefrontal oxygenated hemoglobin (Oxy-Hb), indicative of cortical activation, while performing working memory tasks [1- (baseline), 2-, and 3-back]. Blood glucose levels were continuously measured throughout the conditions. Results revealed no significant changes in Oxy-Hb during the 2-back compared with the 1-back test in any condition, and no time-by-condition interactions. During the 3-back test, there was a significant decrease in Oxy-Hb compared with the 1-back after the WALK condition in the right prefrontal cortex, but there were no time-by-condition interactions, although 3-back reaction time improved only in the WALK condition. Mood and alertness improved after the WALK condition, which was significantly different from the SOCIAL condition. Arterial stiffness moderated the effects, such that changes in Oxy-Hb were significantly different between WALK and SOCIAL conditions only among those with low arterial stiffness. Blood glucose during the interventions did not differ between conditions. Thus, breaking up prolonged sitting with frequent, short physical activity breaks may reduce right prefrontal cortex activation, with improvements in some aspects of working memory, mood, and alertness.

Clinical Trial Registration:www.ClinicalTrials.gov, identifier NCT04137211.
Use of Music Therapy as an Audiological Rehabilitation Tool in the Elderly Population: A Mini-Review
Authors: Grenier Anne Sophie , Lafontaine Louise , Sharp Andréanne
Published: September 2021

It is well known and documented that sensory perception decreases with age. In the elderly population, hearing loss and reduced vestibular function are among the most prevalently affected senses. Two important side effects of sensory deprivation are cognitive decline and decrease in social participation. Hearing loss, vestibular function impairment, and cognitive decline all lead to a decrease in social participation. Altogether, these problems have a great impact on the quality of life of the elderly. This is why a rehabilitation program covering all of these aspects would therefore be useful for clinicians. It is well known that long-term music training can lead to cortical plasticity. Behavioral improvements have been measured for cognitive abilities and sensory modalities (auditory, motor, tactile, and visual) in healthy young adults. Based on these findings, it is possible to wonder if this kind of multisensory training would be an interesting therapy to not only improve communication but also help with posture and balance, cognitive abilities, and social participation. The aim of this review is to assess and validate the impact of music therapy in the context of hearing rehabilitation in older adults. Musical therapy seems to have a positive impact on auditory perception, posture and balance, social integration, and cognition. While the benefits seem obvious, the evidence in the literature is scarce. However, there is no reason not to recommend the use of music therapy as an adjunct to audiological rehabilitation in the elderly when possible. Further investigations are needed to conclude on the extent of the benefits that music therapy could bring to older adults. More data are needed to confirm which hearing abilities can be improved based on the many characteristics of hearing loss. There is also a need to provide a clear protocol for clinicians on how this therapy should be administered to offer the greatest possible benefits.
Multi-Order Brain Functional Connectivity Network-Based Machine Learning Method for Recognition of Delayed Neurocognitive Recovery in Older Adults Undergoing Non-cardiac Surgery
Authors: Wu Guoqing , Jiang Zhaoshun , Cai Yuxi , Zhang Xixue , Lv Yating , Li Shihong , Lin Guangwu , Bao Zhijun , Liu Songbin , Gu Weidong
Published: September 2021

Objectives: Delayed neurocognitive recovery (DNR) seriously affects the post-operative recovery of elderly surgical patients, but there is still a lack of effective methods to recognize high-risk patients with DNR. This study proposed a machine learning method based on a multi-order brain functional connectivity (FC) network to recognize DNR.

Method: Seventy-four patients who completed assessments were included in this study, in which 16/74 (21.6%) had DNR following surgery. Based on resting-state functional magnetic resonance imaging (rs-fMRI), we first constructed low-order FC networks of 90 brain regions by calculating the correlation of brain region signal changing in the time dimension. Then, we established high-order FC networks by calculating correlations among each pair of brain regions. Afterward, we built sparse representation-based machine learning model to recognize DNR on the extracted multi-order FC network features. Finally, an independent testing was conducted to validate the established recognition model.

Results: Three hundred ninety features of FC networks were finally extracted to identify DNR. After performing the independent-sample T test between these features and the categories, 15 features showed statistical differences (P < 0.05) and 3 features had significant statistical differences (P < 0.01). By comparing DNR and non-DNR patients’ brain region connection matrices, it is found that there are more connections among brain regions in DNR patients than in non-DNR patients. For the machine learning recognition model based on multi-feature combination, the area under the receiver operating characteristic curve (AUC), accuracy, sensitivity, and specificity of the classifier reached 95.61, 92.00, 66.67, and 100.00%, respectively.

Conclusion: This study not only reveals the significance of preoperative rs-fMRI in recognizing post-operative DNR in elderly patients but also establishes a promising machine learning method to recognize DNR.
A Quantized Convolutional Neural Network Implemented With Memristor for Image Denoising and Recognition
Authors: Zhang Yuejun , Wu Zhixin , Liu Shuzhi , Guo Zhecheng , Chen Qilai , Gao Pingqi , Wang Pengjun , Liu Gang
Published: September 2021

The interference of noise will cause the degradation of image quality, which can have a negative impact on the subsequent image processing and visual effect. Although the existing image denoising algorithms are relatively perfect, their computational efficiency is restricted by the performance of the computer, and the computational process consumes a lot of energy. In this paper, we propose a method for image denoising and recognition based on multi-conductance states of memristor devices. By regulating the evolution of Pt/ZnO/Pt memristor wires, 26 continuous conductance states were obtained. The image feature preservation and noise reduction are realized via the mapping between the conductance state and the image pixel. Furthermore, weight quantization of convolutional neural network is realized based on multi-conductance states. The simulation results show the feasibility of CNN for image denoising and recognition based on multi-conductance states. This method has a certain guiding significance for the construction of high-performance image noise reduction hardware system.
FLAIR and ADC Image-Based Radiomics Features as Predictive Biomarkers of Unfavorable Outcome in Patients With Acute Ischemic Stroke
Authors: Quan Guanmin , Ban Ranran , Ren Jia-Liang , Liu Yawu , Wang Weiwei , Dai Shipeng , Yuan Tao
Published: September 2021

At present, it is still challenging to predict the clinical outcome of acute ischemic stroke (AIS). In this retrospective study, we explored whether radiomics features extracted from fluid-attenuated inversion recovery (FLAIR) and apparent diffusion coefficient (ADC) images can predict clinical outcome of patients with AIS. Patients with AIS were divided into a training (n = 110) and an external validation (n = 80) sets. A total of 753 radiomics features were extracted from each FLAIR and ADC image of the 190 patients. Interquartile range (IQR), Wilcoxon rank sum test, and least absolute shrinkage and selection operator (LASSO) were used to reduce the feature dimension. The six strongest radiomics features were related to an unfavorable outcome of AIS. A logistic regression analysis was employed for selection of potential predominating clinical and conventional magnetic resonance imaging (MRI) factors. Subsequently, we developed several models based on clinical and conventional MRI factors and radiomics features to predict the outcome of AIS patients. For predicting unfavorable outcome [modified Rankin scale (mRS) > 2] in the training set, the area under the receiver operating characteristic curve (AUC) of ADC radiomics model was 0.772, FLAIR radiomics model 0.731, ADC and FLAIR radiomics model 0.815, clinical model 0.791, and clinical and conventional MRI model 0.782. In the external validation set, the AUCs for the prediction with ADC radiomics model was 0.792, FLAIR radiomics model 0.707, ADC and FLAIR radiomics model 0.825, clinical model 0.763, and clinical and conventional MRI model 0.751. When adding radiomics features to the combined model, the AUCs for predicting unfavorable outcome in the training and external validation sets were 0.926 and 0.864, respectively. Our results indicate that the radiomics features extracted from FLAIR and ADC can be instrumental biomarkers to predict unfavorable clinical outcome of AIS and would additionally improve predictive performance when adding to combined model.
Altered Variability and Concordance of Dynamic Resting-State fMRI Indices in Patients With Attention Deficit Hyperactivity Disorder
Authors: Lou Feiling , Tao Jiejie , Zhou Ronghui , Chen Shuangli , Qian Andan , Yang Chuang , Zheng Xiangwu , Chen Bicheng , Hu Zhishan , Wang Meihao
Published: September 2021

Objective: Attention deficit hyperactivity disorder (ADHD) is a commonly diagnosed neuropsychiatric disorder in children, which is characterized by inattention, hyperactivity and impulsivity. Using resting-state functional magnetic resonance imaging (R-fMRI), the alterations of static and dynamic characteristics of intrinsic brain activity have been identified in patients with ADHD. Yet, it remains unclear whether the concordance among indices of dynamic R-fMRI is altered in ADHD.

Methods: R-fMRI scans obtained from 50 patients with ADHD and 28 healthy controls (HC) were used for the current study. We calculated the regional dynamic changes in brain activity indices using the sliding-window method and compared the differences in variability of these indices between ADHD patients and HCs. Further, the concordance among these dynamic indices was calculated and compared. Finally, the relationship between variability/concordance of these indices and ADHD-relevant clinical test scores was investigated.

Results: Patients with ADHD showed decreased variability of dynamic amplitude of low-frequency fluctuation (dALFF) in the left middle frontal gyrus and increased one in right middle occipital gyrus, as compared with the HCs. Besides, ADHD patients showed decreased voxel-wise concordance in the left middle frontal gyrus. Further, lower voxel-wise concordance in ADHD’s left middle frontal gyrus was associated with more non-perseverative errors in Wisconsin Card Sorting Test, which reflects worse cognitive control.

Conclusion: Our findings suggest that variability and concordance in dynamic brain activity may serve as biomarkers for the diagnosis of ADHD. Further, the decreased voxel-wise concordance is associated with deficit in cognitive control in ADHD patients.