bluuebunny/crossref_metadata_2025 huggingface dataset:
ISPH Simulation of Solitary Waves Propagating Over a Bottom-Mounted Barrier With k–ε Turbulence Model
Authors: Wang Dong , Yan Sheng , Chen Chen , Lin JianGuo , Wang Xupeng , Kazemi Ehsan
Published: December 2021

Solitary wave propagating over a bottom-mounted barrier is simulated using the Incompressible Smoothed Particle Hydrodynamics (ISPH) method in order to study the generation and transport of turbulence associated with flow separation around submerged structures. For an accurate capture of turbulence characteristics during the wave propagation, rather than employing the standard sub-particle scale (SPS) model, the k-ε turbulence model is coupled with the numerical scheme. The results of the numerical model are compared with experimental data, and good agreement is observed in terms of mean velocity, free surface elevation, vorticity fields and turbulent kinetic energy. The numerical model is then employed to investigate the effects of wave non-linearity and geometrical size of the submerged barrier on the flow separation; and calculate the reflection, dissipation and transmission coefficients to evaluate the importance of energy dissipation due to the generation of vortices. The results of this study show that the developed ISPH method with the k-ε turbulence closure model is capable of reproducing the velocity fields and the turbulence characteristics accurately, and thus can be used to perform predictions of comprehensive hydrodynamics of flow-structure interactions in the urban hydro-environment systems.
Do Incubation Temperatures Affect the Preferred Body Temperatures of Hatchling Velvet Geckos?
Authors: Abayarathna Theja , Webb Jonathan K.
Published: December 2021

In many lizards, a mother’s choice of nest site can influence the thermal and hydric regimes experienced by developing embryos, which in turn can influence key traits putatively linked to fitness, such as body size, learning ability, and locomotor performance. Future increases in nest temperatures predicted under climate warming could potentially influence hatchling traits in many reptiles. In this study, we investigated whether future nest temperatures affected the thermal preferences of hatchling velvet geckos, Amalosia lesueurii. We incubated eggs under two fluctuating temperature treatments; the warm treatment mimicked temperatures of currently used communal nests (mean = 24.3°C, range 18.4–31.1°C), while the hot treatment (mean = 28.9°C, range 20.7–38.1°C) mimicked potential temperatures likely to occur during hot summers. We placed hatchlings inside a thermal gradient and measured their preferred body temperatures (Tbs) after they had access to food, and after they had fasted for 5 days. We found that hatchling feeding status significantly affected their preferred Tbs. Hatchlings maintained higher Tbs after feeding (mean = 30.6°C, interquartile range = 29.6–32.0°C) than when they had fasted for 5 d (mean = 25.8°C, interquartile range = 24.7–26.9°C). Surprisingly, we found that incubation temperatures did not influence the thermal preferences of hatchling velvet geckos. Hence, predicting how future changes in nest temperatures will affect reptiles will require a better understanding of how incubation and post-hatchling environments shape hatchling phenotypes.
Programmable Base Editing in Mycobacterium tuberculosis Using an Engineered CRISPR RNA-Guided Cytidine Deaminase
Authors: Ding Xin-Yuan , Li Si-Shang , Geng Yi-Man , Yan Mei-Yi , Li Guo-Bao , Zhang Guo-Liang , Sun Yi-Cheng
Published: December 2021

Multidrug-resistant Mycobacterium tuberculosis (Mtb) infection seriously endangers global human health, creating an urgent need for new treatment strategies. Efficient genome editing tools can facilitate identification of key genes and pathways involved in bacterial physiology, pathogenesis, and drug resistance mechanisms, and thus contribute to the development of novel treatments for drug-resistant tuberculosis. Here, we report a two-plasmid system, MtbCBE, used to inactivate genes and introduce point mutations in Mtb. In this system, the assistant plasmid pRecX-NucSE107A expresses RecX and NucSE107A to repress RecA-dependent and NucS-dependent DNA repair systems, and the base editor plasmid pCBE expresses a fusion protein combining cytidine deaminase APOBEC1, Cas9 nickase (nCas9), and uracil DNA glycosylase inhibitor (UGI). Together, the two plasmids enabled efficient G:C to A:T base pair conversion at desired sites in the Mtb genome. The successful development of a base editing system will facilitate elucidation of the molecular mechanisms underlying Mtb pathogenesis and drug resistance and provide critical inspiration for the development of base editing tools in other microbes.
Genetic Diversity, Structure, and Selective Sweeps in Spinacia turkestanica Associated With the Domestication of Cultivated Spinach
Authors: Gyawali Sanjaya , Bhattarai Gehendra , Shi Ainong , Kik Chris , du Toit Lindsey J.
Published: December 2021

Genotype-by-sequencing (GBS) was used to explore the genetic diversity and structure of Spinacia turkestanica, and the selective sweeps involved in domestication of cultivated spinach, S. oleracea, from S. turkestanica. A total 7,065 single nucleotide polymorphisms (SNPs) generated for 16 Spinacia oleracea and 76 S. turkestanica accessions placed the S. oleracea accessions in one group, Q1, and the 76 S. turkestanica accessions, which originated from Central Asia, in two distinct groups, Q2 and Q3. The Q2 group shared greater genetic identity with the S. oleracea accessions, Q1, than the Q3 S. turkestanica group. Likewise, the S. oleracea Q1 group had a smaller Fst (0.008) with the Q2 group than with the Q3 group (Fst = 0.012), and a greater gene flow (Nm = 30.13) with the Q2 group than with the Q3 group (Nm = 21.83). The Q2 accessions originated primarily from Uzbekistan while the Q3 accessions originated mostly from Tajikistan. The Zarafshan Mountain Range appears to have served as a physical barrier that largely separated members of the Q2 and Q3 groups of S. turkestanica. Accessions with admixtures of Q2 and Q3 were collected primarily from lower elevations at the southern end of the Zarafshan Mountain Range in Uzbekistan. Selective sweep regions identified at 32, 49, and 52 Mb on chromosomes 1, 2, and 3, respectively, appear to have played a vital role in the domestication of S. oleracea as they are correlated with important domestication traits, including day length sensitivity for bolting (flowering). High XP-CLR scores at the 52 Mb genomic region of chromosome three suggest that a selective sweep at this region was responsible for early differentiation of S. turkestanica into two groups in Central Asia.
Structural Characterization of the Highly Restricted Down Syndrome Critical Region on 21q22.13: New KCNJ6 and DSCR4 Transcript Isoforms
Authors: Antonaros Francesca , Pitocco Margherita , Abete Domenico , Vione Beatrice , Piovesan Allison , Vitale Lorenza , Strippoli Pierluigi , Caracausi Maria , Pelleri Maria Chiara
Published: December 2021

Down syndrome (DS) is caused by trisomy of chromosome 21 and it is the most common genetic cause of intellectual disability (ID) in humans. Subjects with DS show a typical phenotype marked by facial dysmorphisms and ID. Partial trisomy 21 (PT21) is a rare genotype characterized by the duplication of a delimited chromosome 21 (Hsa21) portion and it may or may not be associated with DS diagnosis. The highly restricted Down syndrome critical region (HR-DSCR) is a region of Hsa21 present in three copies in all individuals with PT21 and a diagnosis of DS. This region, located on distal 21q22.13, is 34 kbp long and does not include characterized genes. The HR-DSCR is annotated as an intergenic region between KCNJ6-201 transcript encoding for potassium inwardly rectifying channel subfamily J member 6 and DSCR4-201 transcript encoding Down syndrome critical region 4. Two transcripts recently identified by massive RNA-sequencing (RNA-Seq) and automatically annotated on Ensembl database reveal that the HR-DSCR seems to be partially crossed by KCNJ6-202 and DSCR4-202 isoforms. KCNJ6-202 shares the coding sequence with KCNJ6-201 which is involved in many physiological processes, including heart rate in cardiac cells and circuit activity in neuronal cells. DSCR4-202 transcript has the first two exons in common with DSCR4-201, the only experimentally verified gene uniquely present in Hominidae. In this study, we performed in silico and in vitro analyses of the HR-DSCR. Bioinformatic data, obtained using Sequence Read Archive (SRA) and SRA-BLAST software, were confirmed by Reverse Transcription-Polymerase Chain Reaction (RT-PCR) and Sanger sequencing on a panel of human tissues. Our data demonstrate that the HR-DSCR cannot be defined as an intergenic region. Further studies are needed to investigate the functional role of the new transcripts, likely involved in DS phenotypes.
Key Regulatory Differentially Expressed Genes in the Blood of Atrial Septal Defect Children Treated With Occlusion Devices
Authors: Li Bo-Ning , Tang Quan-Dong , Tan Yan-Lian , Yan Liang , Sun Ling , Guo Wei-Bing , Qian Ming-Yang , Chen Allen , Luo Ying-Jun , Zheng Zhou-Xia , Zhang Zhi-Wei , Jia Hong-Ling , Liu Cong
Published: December 2021

Atrial septal defects (ASDs) are the most common types of cardiac septal defects in congenital heart defects. In addition to traditional therapy, interventional closure has become the main treatment method. However, the molecular events and mechanisms underlying the repair progress by occlusion device remain unknown. In this study, we aimed to characterize differentially expressed genes (DEGs) in the blood of patients treated with occlusion devices (metal or poly-L-lactic acid devices) using RNA-sequencing, and further validated them by qRT-PCR analysis to finally determine the expression of key mediating genes after closure of ASD treatment. The result showed that total 1,045 genes and 1,523 genes were expressed differently with significance in metal and poly-L-lactic acid devices treatment, respectively. The 115 overlap genes from the different sub-analyses are illustrated. The similarities and differences in gene expression reflect that the body response process involved after interventional therapy for ASDs has both different parts that do not overlap and the same part that crosses. The same portion of body response regulatory genes are key regulatory genes expressed in the blood of patients with ASDs treated with closure devices. The gene ontology enrichment analysis showed that biological processes affected in metal device therapy are immune response with CXCR4 genes and poly-L-lactic acid device treatment, and the key pathways are nuclear-transcribed mRNA catabolic process and proteins targeting endoplasmic reticulum process with ribosomal proteins (such as RPS26). We confirmed that CXCR4, TOB1, and DDIT4 gene expression are significantly downregulated toward the pre-therapy level after the post-treatment in both therapy groups by qRT-PCR. Our study suggests that the potential role of CXCR4, DDIT4, and TOB1 may be key regulatory genes in the process of endothelialization in the repair progress of ASDs, providing molecular insights into this progress for future studies.
The Panda-Derived Lactobacillus plantarum G201683 Alleviates the Inflammatory Response in DSS-Induced Panda Microbiota-Associated Mice
Authors: Zhou Yi , Duan Ling , Zeng Yan , Niu Lili , Pu Yang , Jacobs Jonathan P. , Chang Candace , Wang Jie , Khalique Abdul , Pan Kangcheng , Fang Jing , Jing Bo , Zeng Dong , Ni Xueqin
Published: December 2021

Intestinal diseases are one of the main causes of captive giant panda death. Their special dietary habits and gastrointestinal tract structure often lead to intestinal epithelium damage and secondary intestinal infection. The captive giant panda is predisposed to suffer from microbiota dysbiosis due to long-term artificial feeding and antibiotic misuse. However, there are few reported probiotics to treat giant panda enteritis and the associated dysbiosis. This study aims to elucidate the mechanism by which Lactobacillus plantarum G201683 (L. plantarum G83), a promising panda-derived probiotic, exerts a protective effect on intestinal inflammation in the dextran sulfate sodium- (DSS) induced panda microbiota-associated (DPMA) mouse model. The DPMA mouse was generated by antibiotic treatment and 5% DSS drinking water administration to assess the effect of L. plantarum G83 on intestinal inflammation and microbiota in vivo. Our results demonstrated the successful generation of a DPMA mouse model with Enterobacteriaceae enrichment, consistent with the giant panda intestinal microbiota. L. plantarum G83 decreased clinical and histological severity of intestinal inflammation, enhanced intestinal tight junction protein expression (ZO-1, Occludin) and alleviated inflammatory cytokine production (TNF-) in the colon of DPMA mice. The administration of L. plantarum G83 altered the microbiota composition by decreasing pathogen associated taxa such as E. coli and increasing abundance of beneficial bacteria including Bifidobacterium spp. These changes in microbiota composition were associated with an increased concentration of short chain fatty acids (SCFA), reduced NF-κB signaling, and an altered balance of T helper cell subsets. Our findings support L. plantarum G83 as a promising probiotic to treat intestinal inflammation in the giant panda.
Effect of Intranodally Administered Dendritic Cell-Based HIV Vaccine in Combination With Pegylated Interferon α-2a on Viral Control Following ART Discontinuation: A Phase 2A Randomized Clinical Trial
Authors: Leal Lorna , Couto Elvira , Sánchez-Palomino Sonsoles , Climent Núria , Fernández Irene , Miralles Laia , Romero Yolanda , González Tania , Maleno Maria José , Paño Blanca , Pich Judit , Nicolau Carlos , Gatell José Maria , Plana Montserrat , García Felipe ,   the DCV3-RISVAC04 Study Group
Published: December 2021

Introduction

Functional cure has been proposed as an alternative to lifelong antiretroviral therapy and therapeutic vaccines represent one of the most promising approaches.

Materials and Methods

We conducted a double-blind randomized placebo-controlled clinical trial to evaluate the safety, immunogenicity, and effect on viral dynamics of a therapeutic vaccine produced with monocyte-derived dendritic cells (MD-DC) loaded with a high dose of heat-inactivated autologous (HIA) HIV-1 in combination with pegylated interferon alpha 2a (IFNα-2a) in people with chronic HIV-1.

Results

Twenty-nine male individuals on successful ART and with CD4+ ≥450 cells/mm3 were randomized 1:1:1:1 to receive three ultrasound-guided inguinal intranodal immunizations, one every 2 weeks: (1) vaccine ~107 MD-DC pulsed with HIA-HIV-1 (1010 HIV RNA copies) (n = 8); (2) vaccine plus three doses of 180 mcg IFNα-2a at weeks 4–6 (n = 6); (3) placebo = saline (n = 7); and (4) placebo plus three doses of 180 mcg IFNα-2a (n = 8). Thereafter, treatment was interrupted (ATI). Vaccines, IFNα-2a, and the administration procedures were safe and well tolerated. All patients’ viral load rebounded during the 12-week ATI period. According to groups, changes in viral set-point between pre-ART and during ATI were not significant. When comparing all groups, there was a tendency in changes in viral set-point between the vaccine group vs. vaccine + IFNα-2a group (>0.5log10p = 0.05). HIV-1-specific T-cell responses (IFN-ƴ Elispot) were higher at baseline in placebo than in the vaccine group (2,259 ± 535 vs. 900 ± 200 SFC/106 PBMC, p = 0.028). A significant difference in the change of specific T-cell responses was only observed at week 4 between vaccine and placebo groups (694 ± 327 vs. 1,718 ± 282 SFC/106 PBMC, p = 0.04). No effect on T-cell responses or changes in viral reservoir were observed after INFα-2a administration.

Discussion

Results from this study show that intranodally administered DC therapeutic vaccine in combination with IFNα-2a was safe and well-tolerated but had a minimal impact on viral dynamics in HIV-1 chronic infected participants.

Clinical Trial Registration

(www.ClinicalTrials.gov), identifier NCT02767193
Long Non-Coding RNA- Associated Competing Endogenous RNA Axes in T-Cells in Multiple Sclerosis
Authors: Sabaie Hani , Salkhordeh Zoha , Asadi Mohammad Reza , Ghafouri-Fard Soudeh , Amirinejad Nazanin , Askarinejad Behzadi Mahla , Hussen Bashdar Mahmud , Taheri Mohammad , Rezazadeh Maryam
Published: December 2021

Multiple sclerosis (MS) is an immune-mediated demyelinating and degenerative disease with unknown etiology. Inappropriate response of T-cells to myelin antigens has an essential role in the pathophysiology of MS. The clinical and pathophysiological complications of MS necessitate identification of potential molecular targets to understand the pathogenic events of MS. Since the functions and regulatory mechanisms of long non-coding RNAs (lncRNAs) acting as competing endogenous RNAs (ceRNAs) in MS are yet uncertain, we conducted a bioinformatics analysis to explain the lncRNA-associated ceRNA axes to clarify molecular regulatory mechanisms involved in T-cells responses in MS. Two microarray datasets of peripheral blood T-cell from subjects with relapsing-remitting MS and matched controls containing data about miRNAs (GSE43590), mRNAs and lncRNAs (GSE43591) were downloaded from the Gene Expression Omnibus database. Differentially expressed miRNAs (DEmiRNAs), mRNAs (DEmRNAs), and lncRNAs (DElncRNAs) were identified by the limma package of the R software. Protein-protein interaction (PPI) network and module were developed using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) and the Molecular Complex Detection (MCODE) Cytoscape plugin, respectively. Using DIANA-LncBase and miRTarBase, the lncRNA-associated ceRNA axes was constructed. We conducted a Pearson correlation analysis and selected the positive correlations among the lncRNAs and mRNAs in the ceRNA axes. Lastly, DEmRNAs pathway enrichment was conducted by the Enrichr tool. A ceRNA regulatory relationship among Small nucleolar RNA host gene 1 (SNHG1), hsa-miR-197-3p, YOD1 deubiquitinase (YOD1) and zinc finger protein 101 (ZNF101) and downstream connected genes was identified. Pathway enrichment analysis showed that DEmRNAs were enriched in “Protein processing in endoplasmic reticulum” and “Herpes simplex virus 1 infection” pathways. To our knowledge, this would be the first report of a possible role of SNHG1/hsa-miR-197-3p/YOD1/ZNF101 axes in the pathogenesis of MS. This research remarks on the significance of ceRNAs and prepares new perceptions for discovering the molecular mechanism of MS.
Bone Marrow Lymphoid Niche Adaptation to Mature B Cell Neoplasms
Authors: Dumontet Erwan , Mancini Stéphane J. C. , Tarte Karin
Published: December 2021

B-cell non-Hodgkin lymphoma (B-NHL) evolution and treatment are complicated by a high prevalence of relapses primarily due to the ability of malignant B cells to interact with tumor-supportive lymph node (LN) and bone marrow (BM) microenvironments. In particular, progressive alterations of BM stromal cells sustain the survival, proliferation, and drug resistance of tumor B cells during diffuse large B-cell lymphoma (DLBCL), follicular lymphoma (FL), and chronic lymphocytic leukemia (CLL). The current review describes how the crosstalk between BM stromal cells and lymphoma tumor cells triggers the establishment of the tumor supportive niche. DLBCL, FL, and CLL display distinct patterns of BM involvement, but in each case tumor-infiltrating stromal cells, corresponding to cancer-associated fibroblasts, exhibit specific phenotypic and functional features promoting the recruitment, adhesion, and survival of tumor cells. Tumor cell-derived extracellular vesicles have been recently proposed as playing a central role in triggering initial induction of tumor-supportive niches, notably within the BM. Finally, the disruption of the BM stroma reprogramming emerges as a promising therapeutic option in B-cell lymphomas. Targeting the crosstalk between BM stromal cells and malignant B cells, either through the inhibition of stroma-derived B-cell growth factors or through the mobilization of clonal B cells outside their supportive BM niche, should in particular be further evaluated as a way to avoid relapses by abrogating resistance niches.
Native CGRP Neuropeptide and Its Stable Analogue SAX, But Not CGRP Peptide Fragments, Inhibit Mucosal HIV-1 Transmission
Authors: Mariotton Jammy , Sams Anette , Cohen Emmanuel , Sennepin Alexis , Siracusano Gabriel , Sanvito Francesca , Edvinsson Lars , Delongchamps Nicolas Barry , Zerbib Marc , Lopalco Lucia , Bomsel Morgane , Ganor Yonatan
Published: December 2021

Background

The vasodilator neuropeptide calcitonin gene-related peptide (CGRP) plays both detrimental and protective roles in different pathologies. CGRP is also an essential component of the neuro-immune dialogue between nociceptors and mucosal immune cells. We previously discovered that CGRP is endowed with anti-viral activity and strongly inhibits human immunodeficiency virus type 1 (HIV-1) infection, by suppressing Langerhans cells (LCs)-mediated HIV-1 trans-infection in-vitro and mucosal HIV-1 transmission ex-vivo. This inhibition is mediated via activation of the CGRP receptor non-canonical NFκB/STAT4 signaling pathway that induces a variety of cooperative mechanisms. These include CGRP-mediated increase in the expression of the LC-specific pathogen recognition C-type lectin langerin and decrease in LC-T-cell conjugates formation. The clinical utility of CGRP and modalities of CGRP receptor activation, for inhibition of mucosal HIV-1 transmission, remain elusive.

Methods

We tested the capacity of CGRP to inhibit HIV-1 infection in-vivo in humanized mice. We further compared the anti-HIV-1 activities of full-length native CGRP, its metabolically stable analogue SAX, and several CGRP peptide fragments containing its binding C-terminal and activating N-terminal regions. These agonists were evaluated for their capacity to inhibit LCs-mediated HIV-1 trans-infection in-vitro and mucosal HIV-1 transmission in human mucosal tissues ex-vivo.

Results

A single CGRP intravaginal topical treatment of humanized mice, followed by HIV-1 vaginal challenge, transiently restricts the increase in HIV-1 plasma viral loads but maintains long-lasting higher CD4+ T-cell counts. Similarly to CGRP, SAX inhibits LCs-mediated HIV-1 trans-infection in-vitro, but with lower potency. This inhibition is mediated via CGRP receptor activation, leading to increased expression of both langerin and STAT4 in LCs. In contrast, several N-terminal and N+C-terminal bivalent CGRP peptide fragments fail to increase langerin and STAT4, and accordingly lack anti-HIV-1 activities. Finally, like CGRP, treatment of human inner foreskin tissue explants with SAX, followed by polarized inoculation with cell-associated HIV-1, completely blocks formation of LC-T-cell conjugates and HIV-1 infection of T-cells.

Conclusion

Our results show that CGRP receptor activation by full-length CGRP or SAX is required for efficient inhibition of LCs-mediated mucosal HIV-1 transmission. These findings suggest that formulations containing CGRP, SAX and/or their optimized agonists/analogues could be harnessed for HIV-1 prevention.
The Role of Interleukin-6 (IL-6) in the Systemic Inflammatory Response in Xenograft Recipients and in Pig Kidney Xenograft Failure
Authors: Zhang Guoqiang , Iwase Hayato , Li Qi , Yamamoto Takayuki , Jagdale Abhijit , Ezzelarab Mohamed B. , Ayares David , Cooper David K. C. , Hara Hidetaka , Wang Gangcheng
Published: December 2021

Background

In pig-to-baboon transplantation models, there is increasing evidence of systemic inflammation in xenograft recipients (SIXR) associated with pig xenograft failure. We evaluated the relationship between systemic inflammatory factors and pig kidney xenograft failure.

Methods

Baboons received kidney transplants from genetically engineered pigs (n=9), and received an anti-CD40mAb-based (n=4) or conventional (n=5) immunosuppressive regimen. The pig kidney grafts were monitored by measurements of serum creatinine, serum amyloid A (SAA), white blood cell (WBC) and platelet counts, plasma fibrinogen, and pro-inflammatory cytokines (baboon and pig IL-6, TNF-α, IL-1β).

Results

Six baboons were euthanized or died from rejection, and 3 were euthanized for infection. Changes in serum creatinine correlated with those of SAA (r=0.56, p<0.01). Serum baboon IL-6 was increased significantly on day 1 after transplantation and at euthanasia (both p<0.05) and correlated with serum creatinine and SAA (r=0.59, p<0.001, r=0.58, p<0.01; respectively). but no difference was observed between rejection and infection. Levels of serum pig IL-6, TNF-α, IL-1β were also significantly increased on day 1 and at euthanasia, and serum pig IL-6 and IL-1β correlated with serum creatinine and SAA. The level of serum baboon IL-6 correlated with the expression of IL-6 and amyloid A in the baboon liver (r=0.93, p<0.01, r=0.79, p<0.05; respectively).

Conclusion

Early upregulation of SAA and serum IL-6 may indicate the development of rejection or infection, and are associated with impaired kidney graft function. Detection and prevention of systemic inflammation may be required to prevent pig kidney xenograft failure after xenotransplantation.
The South American Advances in Submarine Canyons Studies and Their Link to the Ocean Decade
Authors: Silva Marcos V. B. , Araújo Tereza C. M.
Published: December 2021

Submarine canyons have a relevant role in marine ecosystems. They are responsible for oceanographic conditions such as variability of temperature and salinity, sediment transport, nutrients, and even pollutants amongst marine areas. Submarine canyon studies have been growing and reaching prominence due to their importance in the Blue Economy. Initiatives to promote sustainable development for the ocean have been discussed in the Ocean Decade. Although canyons studies are increasing, how can we integrate these with the Ocean Decade outcomes? Thus, we aim to demonstrate an overview of the advances of submarine canyons studies and their link to the Ocean Decade for South America. We analyzed 160 studies divided into spatiotemporal analysis and study approaches according to the Ocean Decade outcomes. We discuss these articles, building a timeline and argumentative topics considering the advances, and discuss gaps to predict the future of submarine canyons studies in the Ocean Decade and Blue Economy context.
Macrobenthic Mollusca of the Prince Gustav Channel, Eastern Antarctic Peninsula: An Area Undergoing Colonisation
Authors: Anderson Madeline P. B. C. , Fenberg Phillip B. , Griffiths Huw J. , Linse Katrin
Published: December 2021

In 2018 RRSJames Clark Rossinvestigated the marine benthic biodiversity of the Prince Gustav Channel area which separates the eastern coast of the Antarctic Peninsula from James Ross Island. The southern end of this channel had been covered by the Prince Gustav Ice Shelf until its collapse in 1995. Benthic samples were collected by an epibenthic sledge at six stations (200–1,200 m depth) in the channel and adjacent Duse Bay. In total 20,307 live collected mollusc specimens belonging to 50 species and 4 classes (Solenogastres, Bivalvia, Gastropoda, and Scaphopoda) were identified. The area may be characterised by it’s low species richness (ranging from 7 to 39 species per station) but high abundances (specifically of the Scaphopods with 11,331 specimens). The functional traits of the community were dominated by motile development and mobility type. Assemblage analyses of the molluscan species abundances within the Prince Gustav Channel stations sit distinct, with no pattern by depth or location. However, when bivalve assemblages were analysed with reference to the wider Weddell Gyre region (15 stations from 300 to 2,000 m depth), the Prince Gustav Channel sits distinct from the other Weddell Gyre stations with a higher dissimilarity between the deeper or more geographically distant areas. The Prince Gustav Channel is undergoing colonisation following the recent ice shelf collapse. With many Antarctic ice shelves threatened under climate warming, this area, with future monitoring, may serve as a case study of benthic faunal succession.
iTRAQ-Based Quantitative Proteomic Analysis Reveals Toxicity Mechanisms in Chlamys farreri Exposed to Okadaic Acid
Authors: Wang Xin , Wang Dan , Zhang Tianyu , Zhang Qianqian , Zhao Jianmin
Published: December 2021

Okadaic acid (OA), produced by dinoflagellates during harmful algal blooms, is a principal diarrhetic shellfish poisoning toxin. This toxin poses a potential threat to bivalves with economic values. To better understand the toxicity mechanism of OA to bivalves, in this study, oxidative stress biomarkers (superoxide dismutase, SOD; catalase, CAT; glutathione S-transferase, GST; malondialdehyde, MDA) and the expression of detoxification genes (heat shock protein 70, HSP70; heat shock protein 90, HSP90; cytochrome P450, CYP450) were assessed in the gills of scallops Chlamys farreri after 24 h, 48 h and 96 h exposure to OA. In addition, the digestive glands of scallops exposed to OA for 96 h were dissected for an iTRAQ based quantitative proteomic analysis. The results of OA exposure experiments showed that OA induces oxidative stress and significant enhancement of the expression of detoxification genes in scallops. The proteomics analysis revealed that 159 proteins altered remarkably in OA-treated scallops, and these proteins were involved in phagosomes, regulation of actin cytoskeleton, adherens junction, tight junction, and focal adhesion. Amino acid biosynthesis, carbon metabolism, pentose phosphate pathway, fructose and mannose metabolism in the digestive glands were also significantly impacted. Our data shed new insights on the molecular responses and toxicity mechanisms of C. farreri to OA.
The Evolution of Micromechanical Properties for Zr-Based Metallic Glass Induced by Laser Shock Peening
Authors: Li Yansen , Wang Zhitao , Wei Yanpeng , Chen Tianyu , Zhang Chunfeng , Huan Yong , Zhang Kun , Wei Bingchen
Published: December 2021

The micromechanical properties of Zr-based metallic glass (MG) induced by laser shock peening (LSP) were studied through the use of nanoindentation. The serrations in representative load-displacement (P-h) curves exhibited a transformation from stairstep-like to ripple-shaped from untreated zone to shock region, which implied an increase in plastic deformation ability of material after LSP. Significant hardening was also observed in the impact zone, which can be attributed to the effect of compressive residual stress. Both increase in hardness and plastic deformation ability in shock region indicate the excellent effect of LSP on the micromechanical properties of investigated Zr-based MG, which provide a new way to study the deformation mechanism in metallic glasses and a further understanding of plasticization.
Did Climate Change Influence the Emergence, Transmission, and Expression of the COVID-19 Pandemic?
Authors: Gupta Saloni , Rouse Barry T. , Sarangi Pranita P.
Published: December 2021

The human race has survived many epidemics and pandemics that have emerged and reemerged throughout history. The novel coronavirus Severe Acute Respiratory Syndrome SARS-CoV-2/COVID-19 is the latest pandemic and this has caused major health and socioeconomic problems in almost all communities of the world. The origin of the virus is still in dispute but most likely, the virus emerged from the bats and also may involve an intermediate host before affecting humans. Several other factors also may have affected the emergence and outcome of the infection but in this review, we make a case for a possible role of climate change. The rise in industrialization-related human activities has created a marked imbalance in the homeostasis of environmental factors such as temperature and other weather and these might even have imposed conditions for the emergence of future coronavirus cycles. An attempt is made in this review to explore the effect of ongoing climate changes and discuss if these changes had a role in facilitating the emergence, transmission, and even the expression of the COVID-19 pandemic. We surmise that pandemics will be more frequent in the future and more severely impactful unless climate changes are mitigated.
Dietary Fiber Influences Bacterial Community Assembly Processes in the Gut Microbiota of Durco × Bamei Crossbred Pig
Authors: Tang Xianjiang , Zhang Liangzhi , Fan Chao , Wang Lei , Fu Haibo , Ren Shi’en , Shen Wenjuan , Jia Shangang , Wu Guofang , Zhang Yanming
Published: December 2021

Several studies have shown that dietary fiber can significantly alter the composition and structure of the gut bacterial community in humans and mammals. However, few researches have been conducted on the dynamics of the bacterial community assembly across different graded levels of dietary fiber in different gut regions. To address this, 24 Durco × Bamei crossbred pigs were randomly assigned to four experimental chows comprising graded levels of dietary fiber. Results showed that the α-and β-diversity of the bacterial community was significantly different between the cecum and the jejunum. Adding fiber to the chow significantly increased the α-diversity of the bacterial community in the jejunum and cecum, while the β-diversity decreased. The complexity of the bacterial network increased with the increase of dietary fiber in jejunal content samples, while it decreased in cecal content samples. Furthermore, we found that stochastic processes governed the bacterial community assembly of low and medium dietary fiber groups of jejunal content samples, while deterministic processes dominated the high fiber group. In addition, deterministic processes dominated all cecal content samples. Taken together, the variation of gut community composition and structure in response to dietary fiber was distinct in different gut regions, and the dynamics of bacterial community assembly across the graded levels of dietary fiber in different gut regions was also distinct. These findings enhanced our knowledge on the bacterial community assembly processes in gut ecosystems of livestock.
Taxonomy and Functional Diversity in the Fecal Microbiome of Beef Cattle Reared in Brazilian Traditional and Semi-Intensive Production Systems
Authors: Corrêa Patricia Spoto , Jimenez Carolina Rodriguez , Mendes Lucas William , Rymer Caroline , Ray Partha , Gerdes Luciana , da Silva Vagner Ovani , De Nadai Fernandes Elisabete Aparecida , Abdalla Adibe Luiz , Louvandini Helder
Published: December 2021

The importance of beef production for economy of Brazil and the growing demand for animal protein across the globe warrant an improvement in the beef production system. Although most attention has been on modulation of the rumen microbiome to improve ruminant production, the role of the lower gut microbiome in host health and nutrition remains relatively unexplored. This work aimed to investigate the taxonomy and functional variations in the fecal microbiome of Brazilian beef cattle reared in two different production systems using a metagenomic approach. Sixty male beef cattle from six farms representing semi-intensive (I, n = 2) and traditional (T, n = 4) Brazilian beef production systems were enrolled in the study. Shotgun sequencing was used to characterize taxonomic and functional composition and diversity of the microbiome in fecal samples collected from each animal. Fecal samples were analyzed for copper (Cu), lead (Pb), nitrogen (N), phosphorous (P), selenium (Se), and zinc (Zn) and stable isotopes of carbon (13C) and nitrogen (15N). The fecal microbiome was influenced by the beef production systems with greater functional and lower taxonomic diversity in beef cattle feces from I systems compared with that from T systems. The concentration of N, P, and Zn was higher in beef cattle feces from I systems compared with that from T systems and was associated with taxonomic and functional profile of fecal microbiome in I system, suggesting the role of fecal nutrients in shaping system-specific microbiome. Semi-intensive management practices led to a more complex but less connected fecal microbiome in beef cattle. The microbial community in beef cattle feces from I systems was characterized by greater abundance of beneficial bacteria (phylum Firmicutes and butyrate-producing bacteria family Lachnospiraceae and genera Anaerostipes, Blautia, Butyrivibrio, Eubacterium, Roseburia, and Ruminococcus). In addition, the fecal abundance of microbial genes related to immune system, nutrient metabolism, and energy production was greater in beef cattle raised under I systems compared with that under T systems. Findings of the current study suggest that semi-intensive management practices could facilitate the development of a healthier and more efficient fecal microbiome in beef cattle by driving an increase in the abundance of beneficial bacteria and functional genes.
Effects of Dietary Bacillus and Non-starch Polysaccharase on the Intestinal Microbiota and the Associated Changes on the Growth Performance, Intestinal Morphology, and Serum Antioxidant Profiles in Ducks
Authors: Peng Simin , Wang Xin , Wang Yuyu , Lv Tuo , Zhao Haohan , Wang Yanzhou , Zhu Siyuan , Qiu Huajiao , Zeng Jianguo , Dai Qiuzhong , Lin Qian
Published: December 2021

Given the desirable results of using probiotics and enzyme preparations as feed supplements in poultry health, here, the effects ofBacillusand Non-starch Polysaccharase (NSPase) on the growth performance, serum antioxidant profiles, and gut microbial communities of early stage ducks is investigated. A total of 400Zhijiangducks (of similar body weight and 1 day age) was selected and randomly divided into four groups. The feeding period was 28 days. Each group contained 10 replicates of 10 birds. Control group (I) was fed with basal diet, while treatment groups II to IV were fed, respectively, with 150 mg/kg NSPases, 25 mg/kgBacillusprobiotics, and 150 mg/kg NSPases + 25 mg/kgBacillusprobiotics in their basal diet. The results demonstrated that dietaryBacillus(25 mg/kg) increased average final weight, average daily gain (ADG), and decreased the malonaldehyde (MDA) in birds (P< 0.05). DietaryBacillus(25 mg/kg) and NSPases +Bacillus(150 mg/kg + 25 mg/kg) presented much higher glutathione (GSH) and activities of superoxide dismutase (SOD) in birds (P< 0.05). Additionally, as revealed by β-diversity indices and analysis of similarities, dietary NSPases +Bacilluscould affect the ileum microbial abundances and diversities at the genera level (P< 0.05), but it had no effect on the caecal microbiota. Also, 16S rRNA sequencing revealed that dietaryBacillusand NSPases +Bacillusincreased the populations ofRuminococcaceaegenera in the cecum (P< 0.05), andS24-7_groupandLactobacillusgenera in the ileum (P< 0.05). However, dietary NSPases andBacillusalone and in combination could significantly decrease the content ofBacteroidesin the ileum (P< 0.05). According to Spearman correlation analysis, 7 ilea bacterial microbiomes (S24-7 group, Lactobacillus, Subgroup 2, Subgroup 1, Kitasatospora, Candidatus Solibacter, and Akkermansia) were positively correlated with SOD (P< 0.05). In conclusion,Bacillus(25 mg/kg) and NSPases (150 mg/kg) included in the diet could efficiently enhance the growth performance by altered gut microbiota composition at the genera level and antioxidant indices of ducks.
MicroRNA Expression and Intestinal Permeability in Children Living in a Slum Area of Bangladesh
Authors: Rashid Humaira , Siddiqua Towfida J. , Hossain Biplob , Siddique Abdullah , Kabir Mamun , Noor Zannatun , Alam Masud , Ahmed Mamun , Haque Rashidul
Published: December 2021

Introduction: MicroRNAs (miRNAs) are small, non-coding RNAs that post-transcriptionally regulate gene expression. Changes in miRNA expression have been reported in a number of intestinal diseases, in both tissue samples and readily accessible specimens like stools. Pathogenic infections, diet, toxins, and other environmental factors are believed to influence miRNA expression. However, modulation of miRNAs in humans is yet to be thoroughly investigated. In this study, we examined the expression levels of two human miRNAs (miRNA-122 and miRNA-21) in stool samples of a group of Bangladeshi children who had an altered/increased intestinal permeability (IIP).

Methods: Stool samples were collected from children with IIP (L:M > 0.09) and normal intestinal permeability (NIP) (L:M ≤ 0.09). Quantitative PCR was performed to quantify the levels of miRNA-122 and miR-21 in stools. Commercial ELISA kits were used to measure gut inflammatory markers Calprotectin and REG1B. Serum samples were tested using Human Bio-Plex Pro Assays to quantify IL-1β, IL-2, IL-5, IL-10, IL-13, IFN-γ, and TNF-α. Total nucleic acid extracted from stool specimens were used to determine gut pathogens using TaqMan Array Card (TAC) system real-time polymerase chain reaction.

Results: The expression levels of miRNA-122 (fold change 11.6; p < 0.001, 95% CI: 6.14–11.01) and miR-21 (fold change 10; p < 0.001, 95% CI: 5.05–10.78) in stool were upregulated in children with IIP than in children with normal intestinal permeability (NIP). Significant correlations were observed between stool levels of miR-122 and miR-21 and the inflammatory cytokines IL-1β, IL-2, IFN-γ, and TNF-α (p < 0.05). Children with IIP were frequently infected with rotavirus, Campylobacter jejuni, Bacteroides fragilis, adenovirus, norovirus, astrovirus, and various Escherichia coli strains (ETEC_STh, ETEC_STp, EAEC_aaiC, EAEC_aatA) (p < 0.001). miR-122 significantly correlated with the fecal inflammatory biomarkers REG1B (p = 0.015) and Calprotectin (p = 0.030), however miR-21 did not show any correlation with these fecal biomarkers.
AMPK as a Potential Therapeutic Target for Intervertebral Disc Degeneration
Authors: Wang Zhen , Shen Jianxiong , Feng Erwei , Jiao Yang
Published: December 2021

As the principal reason for low back pain, intervertebral disc degeneration (IDD) affects the health of people around the world regardless of race or region. Degenerative discs display a series of characteristic pathological changes, including cell apoptosis, senescence, remodeling of extracellular matrix, oxidative stress and inflammatory local microenvironment. As a serine/threonine-protein kinase in eukaryocytes, AMP-activated protein kinase (AMPK) is involved in various cellular processes through the modulation of cell metabolism and energy balance. Recent studies have shown the abnormal activity of AMPK in degenerative disc cells. Besides, AMPK regulates multiple crucial biological behaviors in IDD. In this review, we summarize the pathophysiologic changes of IDD and activation process of AMPK. We also attempt to generalize the role of AMPK in the pathogenesis of IDD. Moreover, therapies targeting AMPK in alleviating IDD are analyzed, for better insight into the potential of AMPK as a therapeutic target.
Opportunities and Obstacles Associated With Sequential Immune Reconstitution Therapy for Multiple Sclerosis: A Case Report
Authors: Garbo Riccardo , Cutuli Daniela , Lorenzut Simone , Gigli Gian Luigi , Bagatto Daniele , Valente Mariarosaria
Published: December 2021

Cladribine is an effective disease-modifying treatment for relapsing-remitting multiple sclerosis that acts as an immune reconstitution therapy and is administered in a pulsed manner. Despite its efficacy, severe disease reactivation early after treatment represents a serious clinical problem, and clear evidence to guide the management of such a situation is lacking. Here, we describe the case of a patient experiencing considerable disease activity during the 1st year after the initiation of cladribine treatment. The patient was switched to alemtuzumab and, therefore, received double immune reconstitution therapy. Data regarding this approach are lacking, and real-world observations may be of interest. Despite achieving good control of disease activity, we observed several serious infectious complications. Our results suggest that sequential immune reconstitution therapies may be effective; however, at the price of higher susceptibility to infections.
On the Bodily Basis of Human Cognition: A Philosophical Perspective on Embodiment
Authors: Gupta Amitabha Das
Published: December 2021

This paper seeks to show that human cognition cannot be characterised purely in mentalistic term. It has a bodily basis and cognition is thus the product of the interplay between mind, body, and brain. This is how the idea of embodiment and its importance is realised and gets its foothold in both philosophy and cognitive science. This brings a radical change introducing a new framework for philosophy and cognitive science. In this new change philosophy and cognitive science have a special role to play which this paper seeks to explore. Philosophy in its capacity as a conceptual inquiry provides justification for human embodiment on a conceptual ground whereas cognitive science provides the same on an empirical and experimental ground. This brings the two disciplines closer resulting into a new field of inquiry which can be best described as the interface between philosophy and cognitive science. An important consequence that follows from this alignment is that the traditional epistemological distinction between the a priori and the empirical can no longer be rigidly maintained.
Impact of Early-Commenced and Continued Sports Training on the Precuneus in Older Athletes
Authors: Yamashita Masatoshi , Suzuki Maki , Kawagoe Toshikazu , Asano Kohei , Futada Masatoshi , Nakai Ryusuke , Abe Nobuhito , Sekiyama Kaoru
Published: December 2021

Intervention studies on sedentary older adults have demonstrated that commencing physical exercise at an older age has a positive effect on brain structure. Although this suggests that older athletes with lifelong sports training have larger gray matter volume (GMV) in some brain regions compared to age-matched non-athletes, evidence in the literature is scarce. Moreover, it remains unclear whether a larger GMV is associated with training intensity or period of training in life. To address these gaps in the literature, we compared regional brain GMV between 24 older athletes (mean age, 71.4 years; age at the commencement of sports training, 31.2 years, continuous sports training, 40.0 years; current training time, 7.9 h/week) and 24 age-matched non-athletes (mean age, 71.0 years). The period of sports training and the current training time of the athletes were assessed. Both groups were evaluated for physical activity intensity as well as cognitive and motor performance. Although no group differences were noted in cognitive and motor performance, athletes reported higher physical activity intensity than non-athletes. Whole-brain structural analysis revealed a significantly larger GMV in several brain regions in athletes. Notably, the GMV of the precuneus in athletes was positively correlated with earlier commencement of sports training and training duration but was negatively correlated with current training time. Our findings demonstrate that early-commenced and continued sports training predicts structural maintenance of the precuneus in old age. Our results also suggest that excessive training time in old age may have a negative impact on the GMV of the precuneus; thereby delineating how the precuneus is associated with lifelong sports training in older athletes.
Sensory Circuit Remodeling and Movement Recovery After Spinal Cord Injury
Authors: Moreno-López Yunuen , Hollis Edmund R.
Published: December 2021

Restoring sensory circuit function after spinal cord injury (SCI) is essential for recovery of movement, yet current interventions predominantly target motor pathways. Integrated cortical sensorimotor networks, disrupted by SCI, are critical for perceiving, shaping, and executing movement. Corticocortical connections between primary sensory (S1) and motor (M1) cortices are critical loci of functional plasticity in response to learning and injury. Following SCI, in the motor cortex, corticocortical circuits undergo dynamic remodeling; however, it remains unknown how rehabilitation shapes the plasticity of S1-M1 networks or how these changes may impact recovery of movement.