bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamics of transcriptome and chromatin accessibility revealed sequential regulation of potential transcription factors during the brown adipose tissue whitening in rabbits
Authors: Du Kun , Chen Guan-He , Bai Xue , Chen Li , Hu Shen-Qiang , Li Yan-Hong , Wang Guo-Ze , He Jing-Wei , Lai Song-Jia
Published: September 2022

Brown adipose tissue (BAT) represents a valuable target for treating obesity in humans. BAT losses of thermogenic capacity and gains a “white adipose tissue-like (WAT-like)” phenotype (BAT whitening) under thermoneutral environments, which could lead to potential low therapy responsiveness in BAT-based obesity treatments. However, the epigenetic mechanisms of BAT whitening remain largely unknown. In this study, BATs were collected from rabbits at day0 (D0), D15, D85, and 2 years (Y2). RNA-sequencing (RNA-seq) and the assay for transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) were performed to investigate transcriptome and chromatin accessibility of BATs at the four whitening stages, respectively. Our data showed that many genes and chromatin accessible regions (refer to as “peaks”) were identified as significantly changed during BAT whitening in rabbits. The BAT-selective genes downregulated while WAT-selective genes upregulated from D0 to Y2, and the de novo lipogenesis-related genes reached the highest expression levels at D85. Both the highly expressed genes and accessible regions in Y2 were significantly enriched in immune response-related signal pathways. Analysis of different relationships between peaks and their nearby genes found an increased proportion of the synchronous changes between chromatin accessibility and gene expression during BAT whitening. The synergistic changes between the chromatin accessibility of promoter and the gene expression were found in the key adipose genes. The upregulated genes which contained increased peaks were significantly enriched in the PI3K-Akt signaling pathway, steroid biosynthesis, TGF-beta signaling pathway, osteoclast differentiation, and dilated cardiomyopathy. Moreover, the footprinting analysis suggested that sequential regulation of potential transcription factors (TFs) mediated the loss of thermogenic phenotype and the gain of a WAT-like phenotype of BAT. In conclusion, our study provided the transcriptional and epigenetic frameworks for understanding BAT whitening in rabbits for the first time and might facilitate potential insights into BAT-based obesity treatments.
Hydrogen reduction of spent lithium-ion battery cathode material for metal recovery: Mechanism and kinetics
Authors: Huang Zhu , Yu Dawei , Makuza Brian , Tian Qinghua , Guo Xueyi , Zhang Kun
Published: September 2022

Hydrogen reduction is becoming a promising method for recycling lithium-ion battery cathode materials. However, the reaction mechanism and kinetics during hydrogen reduction are unclear, requiring further investigation. Therefore, non-isothermal and isothermal reduction experiments were conducted to evaluate the temperature dependence of the hydrogen reduction kinetics using simultaneous thermogravimetric and differential thermal analysis equipped with mass spectrometry. XRD and SEM were used to characterize the reduction products to understand the underlying reduction mechanisms. The hydrogen reduction profile could be divided into three main stages: decomposition of cathode materials, reduction of the resultant nickel and cobalt oxides, and reduction of LiMnO2 and residual nickel and cobalt oxides. The hydrogen reduction rate increased with increasing temperature, and 800°C was the optimum temperature for separating the magnetic Ni-Co alloy from the non-magnetic manganese oxide particles. The apparent activation energy for the isothermal tests in the range of 500–700°C was 84.86 kJ/mol, and the rate-controlling step was the inward diffusion of H2(g) within each particle. There was an downward progression of the reduction through the material bed for the isothermal tests in the range of 700–900°C, with an apparent activation energy of 51.82 kJ/mol.
Superior prognostic value of right ventricular free wall compared to global longitudinal strain in patients with repaired tetralogy of Fallot
Authors: Gao Ying , Li He , He Lin , Zhang Yanting , Sun Wei , Li Meng , Gao Lang , Lin Yixia , Ji Mengmeng , Lv Qing , Wang Jing , Zhang Li , Xie Mingxing , Li Yuman
Published: September 2022

Objectives

Both right ventricular free wall longitudinal strain (RVFWLS) and right ventricular global longitudinal strain (RVGLS) using two-dimensional speckle tracking echocardiography (2D-STE) has been demonstrated to predict adverse outcomes in patients with repaired tetralogy of Fallot (r-TOF). However, RVGLS may be affected by left ventricular (LV) function owing to the fact that the interventricular septum is also a part of the left ventricle. Therefore, the aim of our study was to compare the predictive value of RVFWLS with that of RVGLS in patients with r-TOF.

Materials and methods

A total of 179 patients with r-TOF were included in this study. RVFWLS, RVGLS, and left ventricle global longitudinal strain (LVGLS) were evaluated by 2D-STE. The adverse clinical events were death or r-TOF-related rehospitalization. Prognostic performance was evaluated by C-statistic and Akaike information criterion (AIC).

Results

Thirty-one patients developed poor outcomes during a median follow-up period of 2.8 years. Compared with patients without end-point events, those with end-point events had higher incidence of moderate/severe pulmonary regurgitation, larger right heart sizes, and lower RV fractional area change (RVFAC), RVFWLS, RVGLS, and LVGLS than those without. Multivariate Cox regression analysis revealed that RVFAC, RVFWLS, RVGLS, and LVGLS were predictive of poor outcomes in patients with r-TOF after adjustment for transannular patch and QRS duration. A Cox model using RVFWLS (C index = 0.876, AIC = 228) was found to predict unfavorable outcomes more accurately than a model with RVGLS (C index = 0.856, AIC = 243), RVFAC (C index = 0.811, AIC = 248), and LVGLS (C index = 0.830, AIC = 248).

Conclusion

Although both RVGLS and RVFWLS are associated with adverse events, RVFWLS provides superior prognostic value than that of RVGLS in patients with r-TOF.
The genetic overlap between osteoporosis and craniosynostosis
Authors: Kague Erika , Medina-Gomez Carolina , Boyadjiev Simeon A. , Rivadeneira Fernando
Published: September 2022

Osteoporosis is the most prevalent bone condition in the ageing population. This systemic disease is characterized by microarchitectural deterioration of bone, leading to increased fracture risk. In the past 15 years, genome-wide association studies (GWAS), have pinpointed hundreds of loci associated with bone mineral density (BMD), helping elucidate the underlying molecular mechanisms and genetic architecture of fracture risk. However, the challenge remains in pinpointing causative genes driving GWAS signals as a pivotal step to drawing the translational therapeutic roadmap. Recently, a skull BMD-GWAS uncovered an intriguing intersection with craniosynostosis, a congenital anomaly due to premature suture fusion in the skull. Here, we recapitulate the genetic contribution to both osteoporosis and craniosynostosis, describing the biological underpinnings of this overlap and using zebrafish models to leverage the functional investigation of genes associated with skull development and systemic skeletal homeostasis.
Skeletal outcomes of patients with osteogenesis imperfecta during drug holiday of bisphosphonates: a real-world study
Authors: Zhang Yongze , Hu Jing , Lin Xiaoyun , Sun Lei , Yan Sunjie , Zhang Qian , Jiang Yan , Wang Ou , Xia Weibo , Xing Xiaoping , Li Mei
Published: September 2022

Purpose

This study aimed to investigate the skeletal outcomes of patients with osteogenesis imperfecta (OI) who received bisphosphonate (BP) treatment and entered drug holiday after achieving an age- and sex-specific bone mineral density (BMD) reference.

Methods

Patients with OI receiving BP treatment were enrolled when they entered drug holidays of BPs. The skeletal outcomes were evaluated in detail during the drug holiday, including BMD, X-ray of the bone, bone fracture incidence, and bone turnover biomarkers. The pathogenic mutations of OI were identified by next-generation sequencing and confirmed by Sanger sequencing.

Results

A total of 149 OI patients (127 juveniles and 22 adults) who entered drug holidays after nearly 4 years of BP treatment were included. Areal BMD at the lumbar spine increased from 0.934 ± 0.151 to 0.990 ± 0.142 g/cm2 and was stable in the second (1.029 ± 0.176 g/cm2) and third years (1.023 ± 0.174 g/cm2) of BP drug holidays, and BMD at the femoral neck, trochanter, and total hip had no significant change, but it was gradually inferior to that of the same-gender juveniles in the second and third years of the drug holiday. BMD at the lumbar spine and proximal hip did not change and was inferior to that of the same-gender adults. The average time of fractures fluctuated from 0.18 to 0.08 per year in juveniles, while only one adult suffered from a fracture during BP drug holidays. Bone turnover markers were in the normal range, except for a mildly high level of β-carboxy-terminal cross-linked telopeptide of type 1 collagen in the juvenile group. A total of 17 (11.4%) patients received BP retreatment because of bone loss during the drug holiday. OI type III and type IV and COL1A2 mutation were correlated to a longer duration of BP treatment to enter drug holidays (all p < 0.05). Old age at initial treatment (OR, 1.056) and OI type III (OR, 10.880) were correlated to a higher risk of BP retreatment.

Conclusions

OI patients will undergo nearly 4 years of BP treatment to achieve drug holidays. During the 3 years of the drug holiday, the patients’ BMD is stable, and fracture incidence does not increase significantly. Patients are more inclined to need retreatment during drug holidays owing to the late start of BP treatment and more severe OI phenotypes.
Pollinator movement activity influences genetic diversity and differentiation of spatially isolated populations of clonal forest herbs
Authors: Feigs Jannis Till , Holzhauer Stephanie I. J. , Huang Siyu , Brunet Jörg , Diekmann Martin , Hedwall Per-Ola , Kramp Katja , Naaf Tobias
Published: September 2022

In agricultural landscapes, forest herbs live in small, spatially isolated forest patches. For their long-term survival, their populations depend on animals as genetic linkers that provide pollen- or seed-mediated gene flow among different forest patches. However, whether insect pollinators serve as genetic linkers among spatially isolated forest herb populations in agricultural landscapes remains to be shown. Here, we used population genetic methods to analyze: (A) the genetic diversity and genetic differentiation of populations of two common, slow-colonizing temperate forest herb species [Polygonatum multiflorum (L.) All. and Anemone nemorosa L.] in spatially isolated populations within three agricultural landscapes in Germany and Sweden and (B) the movement activity of their most relevant associated pollinator species, i.e., the bumblebee Bombus pascuorum (Scopoli, 1,763) and the hoverfly Melanostoma scalare (Fabricus, 1,794), respectively, which differ in their mobility. We tested whether the indicated pollinator movement activity affected the genetic diversity and genetic differentiation of the forest herb populations. Bumblebee movement indicators that solely indicated movement activity between the forest patches affected both genetic diversity and genetic differentiation of the associated forest herb P. multiflorum in a way that can be explained by pollen-mediated gene flow among the forest herb populations. In contrast, movement indicators reflecting the total movement activity at a forest patch (including within-forest patch movement activity) showed unexpected effects for both plant-pollinator pairs that might be explained by accelerated genetic drift due to enhanced sexual reproduction. Our integrated approach revealed that bumblebees serve as genetic linkers of associated forest herb populations, even if they are more than 2 km apart from each other. No such evidence was found for the forest associated hoverfly species which showed significant genetic differentiation among forest patches itself. Our approach also indicated that a higher within-forest patch movement activity of both pollinator species might enhance sexual recruitment and thus diminishes the temporal buffer that clonal growth provides against habitat fragmentation effects.
Cuproptosis patterns and tumor microenvironment in endometrial cancer
Authors: Chen Junfeng , Wang Guocheng , Luo Xiaomei , Zhang Jing , Zhang Yongli
Published: September 2022

Cuproptosis is the most recently discovered mode of cell death. It could affect the metabolism of cancer cells and surrounding infiltrating immune cells. In recent years, many studies have also shown that the tumor microenvironment (TME) plays a critical role in tumor growth and development. Mounting evidence suggests that Cuproptosis would bring unique insights into the development of pharmacological and nonpharmacological therapeutic techniques for cancer prevention and therapy. However, no study has been done on the combination of cuproptosis and TME in any cancer. Herein, we investigated the relationship between cuproptosis-related genes (CRGs), TME, and the prognosis of patients with Uterine Corpus Endometrial Carcinoma (UCEC). We identified three CRGs clusters based on 10 CRGs and three CRGs gene clusters based on 600 differentially expressed genes (DEGs) with significant prognostic differences. Following that, the CRGs score based on DEGs with significant prognostic differences was established to evaluate the prognosis and immunotherapeutic efficacy of UCEC patients. The CRGs score was shown to be useful in predicting clinical outcomes. Patients with a low CRGs score seemed to have a better prognosis, a better immunotherapeutic response, and a higher tumor mutation burden (TMB). In conclusion, our study explored the influence of cuproptosis patterns and TME on the prognosis of cancer patients, thereby improving their prognosis.
Feline microRNAome in ovary and testis: Exploration of in-silico miRNA-mRNA networks involved in gonadal function and cellular stress response
Authors: Amelkina Olga , Silva Andreia M. da , Silva Alexandre R. , Comizzoli Pierre
Published: September 2022

The aim of the study was to perform the first in-depth analysis of miRNAs in ovarian and testicular tissues of the domestic cat, a critical biomedical model. Specifically, potential miRNA involvement was explored in gonadal function, testis development, and cellular stress response to preservation protocols. We performed miRNA-sequencing on 20 ovarian and 20 testicular samples from 15 cats, including different ages and tissue treatments. Using fresh tissues (n = 15), we confirmed gonadal expression of 183 miRNA precursors and discovered additional 52 novel feline candidate precursors. We integrated the mRNA data from our previous study on the same age and treatment groups to create in-silico miRNA-mRNA networks and their functional enrichment, which allows comprehensive exploration into possible miRNA functions in cat gonads. Clusters of miRNAs united by shared differentially expressed mRNA targets are potentially involved in testicular development and spermatogenesis. MicroRNAs could play a significant role in ovarian tissue response to stress from microwave-assisted dehydration, with smaller roles in cellular response to vitrification in both ovary and testis. This new list of miRNAs with potential function in cat gonads is a major step towards understanding the gonadal biology, as well as optimizing fertility preservation protocols.
Characterization of the functional effects of ferredoxin 1 as a cuproptosis biomarker in cancer
Authors: Li Xiang , Dai Zihan , Liu Jincheng , Sun Zhenqian , Li Na , Jiao Guangjun , Cao Hongxin
Published: September 2022

Background: Cuproptosis is a recently discovered form of programmed cell death. Ferredoxin 1 (FDX1) is a key gene that mediates this process. However, the role of FDX1 in human tumors is not clear.

Methods: We comprehensively analyzed the differential expression and genetic alterations of FDX1 using multiomics data from The Cancer Genome Atlas (TCGA) and the Genotype-Tissue Expression (GTEx) database. Subsequently, we explored the association between FDX1 and tumor parameters such as genomic instability, RNA methylation modifications, immune infiltration and pathway activity. In addition, we performed functional enrichment analysis and assessed the sensitivity potential of FDX1-related drugs. Finally, we experimentally verified the functional effects of FDX1.

Results: The analysis revealed differential expression of FDX1 in a variety of tumors. By analyzing the association of FDX1 expression with genomic instability, immune cell infiltration, signaling pathway etc. We explored the role of FDX1 in regulating cell activity. Also, we evaluated the function of FDX1 in biologic process and drug sensitivity. Our experimental results demonstrated that FDX1 exerts its antitumor effects through cuproptosis in liver hepatocellular carcinoma and non-small cell lung cancer cell lines.

Conclusion: Our study reveals the functional effects of FDX1 in tumors and deepens the understanding of the effects of FDX1. We validated the inhibitory effect of FDX1 in copper induced cell-death, confirming the role of FDX1 as a cuproptosis biomarker.
The cuproptosis-related signature predicts prognosis and indicates immune microenvironment in breast cancer
Authors: Li Jia , Wu Fei , Li Chaofan , Sun Shiyu , Feng Cong , Wu Huizi , Chen Xi , Wang Weiwei , Zhang Yu , Liu Mengji , Liu Xuan , Cai Yifan , Jia Yiwei , Qiao Hao , Zhang Yinbin , Zhang Shuqun
Published: September 2022

Breast cancer (BC) is the most diagnosed cancer in women. Cuproptosis is new regulated cell death, distinct from known death mechanisms and dependent on copper and mitochondrial respiration. However, the comprehensive relationship between cuproptosis and BC is still blank until now. In the present study, we acquired 13 cuproptosis-related regulators (CRRs) from the previous research and downloaded the RNA sequencing data of TCGA-BRCA from the UCSC XENA database. The 13 CRRs were all differently expressed between BC and normal samples. Using consensus clustering based on the five prognostic CRRs, BC patients were classified into two cuproptosis-clusters (C1 and C2). C2 had a significant survival advantage and higher immune infiltration levels than C1. According to the Cox and LASSO regression analyses, a novel cuproptosis-related prognostic signature was developed to predict the prognosis of BC effectively. The high- and low-risk groups were divided based on the risk scores. Kaplan-Meier survival analysis indicated that the high-risk group had shorter overall survival (OS) than the low-risk group in the training, test and entire cohorts. GSEA indicated that the immune-related pathways were significantly enriched in the low-risk group. According to the CIBERSORT and ESTIMATE analyses, patients in the high-risk group had higher infiltrating levels of antitumor lymphocyte cell subpopulations and higher immune score than the low-risk group. The typical immune checkpoints were all elevated in the high-risk group. Furthermore, the high-risk group showed a better immunotherapy response than the low-risk group based on the Tumor Immune Dysfunction and Exclusion (TIDE) and Immunophenoscore (IPS). In conclusion, we identified two cuproptosis-clusters with different prognoses using consensus clustering in BC. We also developed a cuproptosis-related prognostic signature and nomogram, which could indicate the outcome, the tumor immune microenvironment, as well as the response to immunotherapy.
Platelet-to-lymphocyte ratio at 24h after thrombolysis is a prognostic marker in acute ischemic stroke patients
Authors: Sun Ying-Ying , Wang Mei-Qi , Wang Yan , Sun Xin , Qu Yang , Zhu Hong-Jing , Wang Si-Ji , Yan Xiu-Li , Jin Hang , Zhang Peng , Yang Yi , Guo Zhen-Ni
Published: September 2022

Background

The changes in the platelet-to-lymphocyte ratio (PLR) before and after recombinant tissue plasminogen activator (rtPA) treatment and the time point at which the PLR is a potentially valuable prognostic predictor in patients wit ischemic stroke remain largely unknown. Therefore, the purpose of this study was to explore the characteristics of the PLR and evaluate their effects on clinical outcomes before and 24 h after rtPA treatment.

Methods

This study included 741 consecutive patients with acute ischemic stroke who underwent intravenous thrombolysis with rtPA. We collected data on demographics, vascular risk factors, medication history, and other clinical information pertaining to all patients. Specifically, blood samples for PLR measurement were collected on admission and 24 h after stroke. The outcome was assessed by using the Modified Rankin Scale (mRS) at 3 months and whether death occurred within 3 months or not. Univariate and multivariate logistic regression analysis was used to assess the association of the PLR with the risks of poor outcome (mRS>2) and death. An individualized prediction model was established to predict poor outcome.

Results

Of the 741 patients, 255 (34.4%) had poor outcome, and 43 (5.8%) died. The PLR significantly increased 24 h after rtPA in patients with poor outcome and death. Logistic analysis revealed that higher PLR 24 h after rtPA was independently associated with increased risks of poor outcome and death. However, the PLR on admission was not associated with the risks of poor outcome and death. The individualized prediction model for poor outcome based on the 24-h PLR exhibited favorable discrimination (areas under the curves of the training and validation groups: 0.743 and 0.729, respectively), calibration (P > 0.05), and clinical usefulness.

Conclusions

We found the PLR to be a variable that potentially predicts the risks of poor outcome and death in patients with acute ischemic stroke 24 h after rtPA; however, it cannot make the same prediction on admission.
Identification of hub biomarkers and immune cell infiltration characteristics of polymyositis by bioinformatics analysis
Authors: Jia Qi , Hao Rui-Jin-Lin , Lu Xiao-Jian , Sun Shu-Qing , Shao Jun-Jie , Su Xing , Huang Qing-Feng
Published: September 2022

Background

Polymyositis (PM) is an acquirable muscle disease with proximal muscle involvement of the extremities as the main manifestation; it is a category of idiopathic inflammatory myopathy. This study aimed to identify the key biomarkers of PM, while elucidating PM-associated immune cell infiltration and immune-related pathways.

Methods

The gene microarray data related to PM were downloaded from the Gene Expression Omnibus database. The analyses using Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes, gene set enrichment analysis (GSEA), and protein-protein interaction (PPI) networks were performed on differentially expressed genes (DEGs). The hub genes of PM were identified using weighted gene co-expression network analysis (WGCNA) and least absolute shrinkage and selection operator (LASSO) algorithm, and the diagnostic accuracy of hub markers for PM was assessed using the receiver operating characteristic curve. In addition, the level of infiltration of 28 immune cells in PM and their interrelationship with hub genes were analyzed using single-sample GSEA.

Results

A total of 420 DEGs were identified. The biological functions and signaling pathways closely associated with PM were inflammatory and immune processes. A series of four expression modules were obtained by WGCNA analysis, with the turquoise module having the highest correlation with PM; 196 crossover genes were obtained by combining DEGs. Subsequently, six hub genes were finally identified as the potential biomarkers of PM using LASSO algorithm and validation set verification analysis. In the immune cell infiltration analysis, the infiltration of T lymphocytes and subpopulations, dendritic cells, macrophages, and natural killer cells was more significant in the PM.

Conclusion

We identified the hub genes closely related to PM using WGCNA combined with LASSO algorithm, which helped clarify the molecular mechanism of PM development and might have great significance for finding new immunotherapeutic targets, and disease prevention and treatment.
What is the optimal duration of immune checkpoint inhibitors in malignant tumors?
Authors: Yin Jiaxin , Song Yuxiao , Tang Jiazhuo , Zhang Bicheng
Published: September 2022

Immunotherapy, represented by immune checkpoint inhibitors (ICIs), has made a revolutionary difference in the treatment of malignant tumors, and considerably extended patients’ overall survival (OS). In the world medical profession, however, there still reaches no clear consensus on the optimal duration of ICIs therapy. As reported, immunotherapy response patterns, immune-related adverse events (irAEs) and tumor stages are all related to the diversity of ICIs duration in previous researches. Besides, there lacks clear clinical guidance on the intermittent or continuous use of ICIs. This review aims to discuss the optimal duration of ICIs, hoping to help guide clinical work based on the literature.
Video surveys of sea snakes in the mesophotic zone shed light on trends in populations
Authors: Speed Conrad W. , Wilson Nerida G. , Somaweera Ruchira , Udyawer Vinay , Meekan Mark G. , Whisson Corey , Miller Karen
Published: September 2022

Declines in abundance of sea snakes have been observed on reefs throughout the Indo-Pacific, although the reasons are unknown. To date, surveys have occurred on shallow reefs, despite sea snakes occurring over a large depth range. It is not known if populations of sea snakes in deep habitats have undergone similar declines. To address this, we analysed deep-water video data from a historical hotspot of sea snake diversity, Ashmore Reef, in 2004, 2016, and 2021. We collected 288 hours of video using baited remote underwater videos and a remotely operated vehicle at depths between 13 and 112 m. We observed 80 individuals of seven species with Aipysurus laevis (n = 30), Hydrophis peronii (n = 8), and H. ocellatus (n = 6) being the most abundant. Five of the species (A. duboisii, A. apraefrontalis, H. ocellatus, H. kingii, and Emydocephalus orarius) had not been reported in shallow waters for a decade prior to our study. We found no evidence of a decline in sea snakes across years in deep-water surveys, although abundances were lower than those in early shallow-water surveys. A comparison of BRUVS data from 2004 and 2016 was consistent with the hypothesis that predation by sharks may have contributed to the loss of sea snakes in shallow habitats. Our study highlights the use of underwater video to collect information on sea snakes in the mesophotic zone and also suggests that future monitoring should include these depths in order to capture a more complete representation of habitats occupied.
The invasive alga Gracilaria vermiculophylla in the native northwest Pacific under ocean warming: Southern genetic consequence and northern range expansion
Authors: Liu Yi-Jia , Zhong Kai-Le , Jueterbock Alexander , Satoshi Shimada , Choi Han-Gil , Weinberger Florian , Assis Jorge , Hu Zi-Min
Published: September 2022

Ocean warming is one of the most important factors in shaping the spatial distribution and genetic biodiversity of marine organisms worldwide. The northwest Pacific has been broadly illustrated as an essential seaweed diversity hotspot. However, few studies have yet investigated in this region on whether and how past and ongoing climate warming impacted the distribution and genetic pools of coastal seaweeds. Here, we chose the invasive species Gracilaria vermiculophylla as a model, and identified multiple genetic lineages in the native range through genome-scale microsatellite genotyping. Subsequently, by reconstructing decadal trends of sea surface temperature (SST) change between 1978 and 2018, we found that SST in northern Japan and the East China Sea indeed increased broadly by 0.25-0.4°C/decade. The projections of species distribution models (SDMs) under different future climate change scenarios (RCP 2.6, RCP 4.5, RCP 6.0 and RCP 8.5) indicated that a unique genetic pool of G. vermiculophylla at its current southern range limit (i.e. the South China Sea) is at high risk of disappearance, and that the populations at its current northern range limit (i.e. in Hokkaido region) will undergo poleward expansions, particularly by the year 2100. Such responses, along with this species’ limited dispersal potential, may considerably alter the contemporary distribution and genetic composition of G. vermiculophylla in the northwest Pacific, and ultimately threaten ecological services provided by this habitat-forming species and other associated functional roles.
Effect of industrial waste molecular sieves on internally cured cement-based materials
Authors: Shi Peng , Li Zhen , Chen Xiaorun , Zeng Lei , Hu Rong
Published: September 2022

Using waste molecular sieves (MS) instead of sand as water-absorbing fine aggregates in cement-based materials can effectively deal with factory adsorption waste and reduce sand consumption. In this article, the industrial waste molecular sieve is recycled and incorporated into cement-based materials. The effect of the molecular sieve as a hydration internal curing agent on the performance of cement-based materials is studied. A series of experiments are designed to find out the appropriate ratio and to evaluate and analyze the internal curing effect of waste molecular sieves. Compressive strength, flexural strength, and dry shrinkage properties of mortar with different dosages of the molecular sieve are tested. The water release behavior of the molecular sieve in mortar is comprehensively analyzed combined with the desorption test of the molecular sieve. Results show that the compressive and flexural strength increase by 5% and 10%, respectively, and the drying shrinkage decrease by 6% when 10% of sand is replaced by a molecular sieve under the same total water content. The hydration behavior of the sample is characterized by a microcosmic test of paste. Thermogravimetric analysis is used to calculate the content of corresponding hydration products and quantitatively describe the hydration degree of the internal curing paste mixed with MS. Results show that the content of hydration products is improved by the addition of the molecular sieve, which provides a theoretical basis for the enhancement of mortar to a certain extent.
Synthesis of a novel flame retardant with phosphaphenanthrene and phosphazene double functional groups and flame retardancy of poly (lactic acid) composites
Authors: Bao Dong Mei , Wang Jian Hang , Hou Ze Ming , Xu Zhi Yan , Ye Xiao Lin , Qi Yu Zhao , Xu Song Jiang , Long Li Juan , Wu Zhong Li , Wen Zhu
Published: September 2022

A novel flame retardant hexa (4- (9,10-dihydro-9-oxa-10-phosphaphenanthrene-10 -sulfide)-hydroxymethylphenoxy) cyclotriphosphazene (HAP-DOPS) with double functional groups was synthesized, and poly (lactic acid) (PLA) composites were prepared by melt extrusion. The flame retardancy and thermal degradation behavior of flame retardant PLA composites were studied by limiting oxygen index (LOI), vertical burning test (UL-94), cone calorimeter test (CCT), and thermogravimetric-infrared spectroscopy analysis (TG-IR). The experimental results showed that HAP-DOPS had a good flame-retardant effect on PLA. At flame retardant content of 5 wt%, the PLA/HAP-DOPS composite achieved a V-0 rating (UL-94, 3.2 mm) and a LOI value of 26.6%. The heat release rate (HRR) and total heat release (THR) of PLA composites were decreased by adding HAP-DOPS. The flame retardancy index (FRI) of PLA/HAP-DOPS-7.5 wt% was 1.0257, which showed good flame retardancy. The results of TG-IR showed that HAP-DOPS mainly had a gas-phase flame-retardant effect in PLA.
Predictive features of central lymph node metastasis in papillary thyroid microcarcinoma: Roles of active surveillance in over-treatment
Authors: Han Bo , Hao Sen , Wu Jixiang , Fang Jugao , Han Zhengxue
Published: September 2022

Background

Low-risk papillary thyroid microcarcinoma (PTMC) without clinically evident lymph nodes, extrathyroidal expansions, and distant metastases may be candidates for active monitoring.

Objective

The purpose of this research is to identify risk factors for papillary thyroid microcarcinoma (PTMC) metastasis to central cervical lymph nodes (CLNM) and to discuss the viability of an active surveillance strategy to minimize unnecessary therapy for patients.

Methods

This single-center retrospective study was conducted on the data and medical records of the patients who were diagnosed with PTMC and underwent surgery at the Baotou Cancer Hospital, China, between January 1, 2018, and December 31, 2019. Both lobectomy and complete thyroid resections were performed, and central lymph node dissections (CLND) were used in all patients. Comparisons and analyses were conducted on the preoperative ultrasound (US) characteristics, the post-operation pathological results, and lymph node metastasis.

Results

We analyzed 172 patients with PTMC with average age 48.32 ± 10.59 years old, with 31 males and 142 females. US testing showed 74 (43.0%) patients had suspicious lymph nodes; 31 (41.9%) had capsular invasion and 52 (30.2%) patients were confirmed to have CLNM. Based on logistic regression analysis, central lymph node metastasis was shown to be more common in individuals with PTMC who were older than 45 years old, male, and had tumors that lacked micro-calcification on US imaging. Postoperative pathology assessments suggested that 58 cases (33.7%) were more suitable candidates for active surveillance cohorts.

Conclusions

While active surveillance might benefit many PTMC patients, treatments for the patients should also encompass occult lymph node metastasis, especially in patients with over 45 years old, male, tumor without micro-calcification in the US imaging. Furthermore, the prediction of lymph nodes in the central cervical via the preoperative US and the PTMC risk stratification accuracy need to be improved. Our findings showed about 30% of the patients with PTMC had no active surveillance high-risk factors but required surgical treatment. Fear of cancer in the PTMC patients, although informed of the details, is still the main reason for choosing surgical treatment over active surveillance.
Ultrasound response to tofacitinib in patients with rheumatoid arthritis: Data from a multicenter 24 weeks prospective study
Authors: Germanò Giuseppe , Macchioni Pierluigi , Maranini Beatrice , Ciancio Giovanni , Bonazza Sara , Govoni Marcello , Salvarani Carlo
Published: September 2022

Background

Treatment of rheumatoid arthritis (RA) should aim at full remission. Ultrasonography (US) might have an added value to clinical examination in assessing disease activity of RA. In this study we evaluated the ultrasound response, next to clinical and laboratory response, in RA patients treated with tofacitinib (TOF).

Methods

In this observational multicenter study, patients received TOF 5 mg twice daily, with or without the contemporary use of methotrexate or other conventional DMARD, for 24 weeks. All patients underwent clinical, laboratory and US examinations of 40 sites among joints and tendons. Sonographers were blinded to clinical and laboratory parameters. Data were assessed at baseline, week 2, 4, 8, 12 and 24. For each patient we used two US joint scores (Gray Scale –GS–and power Doppler –PD– score), a 0–3 semi-quantitative scale for each joint and the EULAR-OMERACT US scoring system (combined GS and PD graded from 0 to 3). Besides, we calculated a tenosynovitis scores (GS and PD) according to the OMERACT score.

Results

Fifty-two RA patients completed the 6 months period study: mean disease duration 9.97 ± 8.75 years, baseline DAS28-CRP 4.9 ± 1.2, HAQ 1.4 ± 0.7, C-reactive protein (CRP 2.25 ± 3.11 mg/dl). Baseline joint (GS, PD and combined-US) and tendon US scores (GS and PD) were 23.5 ± 18.4, 22.7 ± 19.3, 25.7 ± 20.6, 10.5 ± 11.4 and 11.0 ± 12.0, respectively. US joint and tendon scores significantly reduced as early as T1 (week 2) examination as well as at week 4, 12 and 24, as compared to baseline values (p < 0.001 for all comparisons). Improvement of joint US scores (GS, PD and US-combined) correlated at T4 examination, with the reduction of serum CRP levels (rho 0.418, p = 0.036, rho 0.495, p = 0.004 and rho 0.454, p = 0.009, respectively). We did not find any correlation between the variations of DAS28-CRP and any US scores at any visits.

Conclusion

These results provide evidence that TOF treatment leads to early (2 weeks) and persistent reduction of US signs of inflammation both at tendon and joint level comparable to clinical improvement.
Development versus predation: Transcriptomic changes during the lifecycle of Myxococcus xanthus
Authors: Pérez Juana , Contreras-Moreno Francisco Javier , Muñoz-Dorado José , Moraleda-Muñoz Aurelio
Published: September 2022

Myxococcus xanthus is a multicellular bacterium with a complex lifecycle. It is a soil-dwelling predator that preys on a wide variety of microorganisms by using a group and collaborative epibiotic strategy. In the absence of nutrients this myxobacterium enters in a unique developmental program by using sophisticated and complex regulatory systems where more than 1,400 genes are transcriptional regulated to guide the community to aggregate into macroscopic fruiting bodies filled of environmentally resistant myxospores. Herein, we analyze the predatosome of M. xanthus, that is, the transcriptomic changes that the predator undergoes when encounters a prey. This study has been carried out using as a prey Sinorhizobium meliloti, a nitrogen fixing bacteria very important for the fertility of soils. The transcriptional changes include upregulation of genes that help the cells to detect, kill, lyse, and consume the prey, but also downregulation of genes not required for the predatory process. Our results have shown that, as expected, many genes encoding hydrolytic enzymes and enzymes involved in biosynthesis of secondary metabolites increase their expression levels. Moreover, it has been found that the predator modifies its lipid composition and overproduces siderophores to take up iron. Comparison with developmental transcriptome reveals that M. xanthus downregulates the expression of a significant number of genes coding for regulatory elements, many of which have been demonstrated to be key elements during development. This study shows for the first time a global view of the M. xanthus lifecycle from a transcriptome perspective.
Complete genome sequences of classical swine fever virus: Phylogenetic and evolutionary analyses
Authors: Liu Yue , Bahoussi Amina Nawal , Wang Pei-Hua , Wu Changxin , Xing Li
Published: September 2022

The classical swine fever virus (CSFV) outbreaks cause colossal losses of pigs and drastic economic impacts. The current phylogenetic CSFV groups were determined mainly based on the partial genome. Herein, 203 complete genomic sequences of CSFVs collected worldwide between 1998 and 2018 available on the GenBank database were retrieved for re-genotyping and recombination analysis. The maximum likelihood phylogenetic tree determined two main groups, GI and GII, with multiple sub-genotypes. The “strain 39” (GenBank ID: AF407339), previously identified as belonging to sub-genotypes 1.1 or 2.2 based on the partial sequences, is found to be genetically distinct and independent, forming a new lineage depicted as GI-2.2b. Ten potential natural recombination events were identified, seven of which were collected in China and found involved in the genetic diversity of CSFVs. Importantly, the vaccine strains and highly virulent strains were all involved in the recombination events, which would induce extra challenges to vaccine development. These findings alarm that attenuated vaccines should be applied with discretion and recommend using subunit vaccines in parallel with other preventive strategies for better management of CSFVs.
Isolation and characterization of phosphate solubilizing bacteria naturally colonizing legumes rhizosphere in Morocco
Authors: Janati Walid , Mikou Karima , El Ghadraoui Lahsen , Errachidi Faouzi
Published: September 2022

Low-cost and environmentally friendly agricultural practices have received increasing attention in recent years. Developing microbial inoculants containing phosphate (P) solubilizing bacteria (PSB) represents an emerging biological solution to improve rhizosphere P availability. The present study aims to explore PSB strains isolated from soils located at different bioclimatic stages in Morocco and present in various legumes rhizosphere to improve agronomic microbial fertilizer’s effectiveness. It was also aimed to test the isolated strains for their ability to solubilize P in NBRIP medium with Tricalcium P (Ca3 (PO4)2) (TCP), rock phosphate (RP), and their combination as a source of phosphorus, by (22) experiment design. Bacterial strains with a high P solubility index (PSI) were selected, characterized, and compared to commercial control. The vanadate-molybdate method was used to estimate P solubilization activity. Stress tolerance to salinity, acidity, drought, and temperature was tested. From all isolated strains (64), 12 were screened as promising biotechnological interest because of their P solubilization and their good resistance to different drastic conditions. Besides, the strain WJEF15 showed the most P solubility efficiency in NBRIP solid medium with a PSI of 4.1; while the WJEF61 strain was located as the most efficient strain in NBRIP-TCP liquid medium by releasing 147.62 mg.l–1 of soluble P. In contrast, in the NBRIP-RP medium, the strain WJEF15 presented maximum solubilization with 25.16 mg.l–1. The experiment design showed that a combination of RP and TCP with max level progressively increases P solubilization by 20.58%, while the WJEF63 strain has the most efficient concentration of 102.69 mg.l–1. Indeed, among the selected strains, four strains were able to limit tested fungi growth. Thus, results reveal a potential effect of selecting PSBs to support cropping cultures as plant growth-promoting rhizobacteria (PGPR).
Exopolysaccharide composition and size in Sulfolobus acidocaldarius biofilms
Authors: Kuschmierz Laura , Meyer Martin , Bräsen Christopher , Wingender Jost , Schmitz Oliver J. , Siebers Bettina
Published: September 2022

Extracellular polymeric substances (EPS) comprise mainly carbohydrates, proteins and extracellular DNA (eDNA) in biofilms formed by the thermoacidophilic Crenarchaeon Sulfolobus acidocaldarius. However, detailed information on the carbohydrates in the S. acidocaldarius biofilm EPS, i.e., the exopolysaccharides (PS), in terms of identity, composition and size were missing. In this study, a set of methods was developed and applied to study the PS in S. acidocaldarius biofilms. It was initially shown that addition of sugars, most significantly of glucose, to the basal N-Z-amine-based growth medium enhanced biofilm formation. For the generation of sufficient amounts of biomass suitable for chemical analyses, biofilm growth was established and optimized on the surface of membrane filters. EPS were isolated and the contents of carbohydrates, proteins and eDNA were determined. PS purification was achieved by enzymatic digestion of other EPS components (nucleic acids and proteins). After trifluoroacetic acid-mediated hydrolysis of the PS fraction, the monosaccharide composition was analyzed by reversed-phase liquid chromatography (RP-LC) coupled to mass spectrometry (MS). Main sugar constituents detected were mannose, glucose and ribose, as well as minor proportions of rhamnose, N-acetylglucosamine, glucosamine and galactosamine. Size exclusion chromatography (SEC) revealed the presence of one single PS fraction with a molecular mass of 4-9 × 104 Da. This study provides detailed information on the PS composition and size of S. acidocaldarius MW001 biofilms and methodological tools for future studies on PS biosynthesis and secretion.
Potential application of the probiotic Bacillus licheniformis as an adjuvant in the treatment of diseases in humans and animals: A systematic review
Authors: Ramirez-Olea Hugo , Reyes-Ballesteros Bernardo , Chavez-Santoscoy Rocio Alejandra
Published: September 2022

The use of Bacillus licheniformis as a probiotic has increased significantly in recent years. Published reports demonstrate that it provides multiple benefits for health. Although there are already studies in humans and is marketed, it is mostly used in the veterinary industry still. However, its benefits could be extrapolated to humans in future. This review addresses the application of B. licheniformis, its sporulation, mechanisms of action, and its role in the resolution, treatment, and prevention of different conditions and diseases. It focuses on scientific advances from 2016 to mid-2022 and emphasizes the most common diseases in the general population. Most of the 70% of published studies about the health benefits of B. licheniformis have been published from 2016 until now. The intake of B. licheniformis has been related to the effects of modulation of the intestinal microbiota, antimicrobial activity, growth promotion, anti-inflammatory and immunostimulatory effects, promotion of the regulation of the lipid profile, increase of neurotransmitters, and stress reduction, among others. These results provide novel possible applications of this and other probiotics in general. Although many benefits can be reported on a microorganism, the combination with others could provide a better effect. Further studies like this need to be done to understand the specific advantages of each probiotic and its strains and therefore achieve a better selection of them for a specific disease or disorder.
Identification and characterization of a novel metallo β-lactamase, SZM-1, in Shenzhen Bay, South China
Authors: Fang Lingxu , Liu Zongbao , Lu Zhongyi , Huang Rongzhong , Xiang Rong
Published: September 2022

Metallo β-Lactamases (MBLs) degrade most clinical β-lactam antibiotics, especially Carbapenem, posing a huge threat to global health. Studies on environmental MBLs are important for risk assessment of the MBLs transmission among connected habitats, and between environment and human. Here, we described a novel metallo β-Lactamases, named SZM-1 (Shenzhen metallo-β-lactamase), from an Arenimonas metagenome-assembled genome recovered from the river sediment in the Shenzhen Bay area, south China. Phylogenetic analysis, primary sequence comparison, structural modeling suggested that the SZM-1 belongs to B1 MBL family, likely harboring a typical di-zinc catalytic center. Furthermore, the gene encoding the MBLs was cloned into Escherichia coli TOP10 for Carba NP test and antimicrobial susceptibility test. The results indicated that the SZM-1 had carbapenemase activity, and conferred the carrier to increased resistance toward carbapenems. Taken together, our results raise alarms about the emergence and spread of the SZM-1, and suggest further surveillance, especially in hospital settings and clinical isolates, to determine whether blaSZM–1 is a mobilizable antibiotic resistance.