bluuebunny/crossref_metadata_2025 huggingface dataset:
Correlated evolution of wing morphology and echolocation calls in bats
Authors: Zou Wenyu , Liang Haiying , Wu Pan , Luo Bo , Zhou Daying , Liu Wenqin , Wu Jiashu , Fang Linjie , Lei Yudie , Feng Jiang
Published: December 2022

Introduction

Flight and echolocation are two crucial behaviors associated with niche expansion in bats. Previous researches have attempted to explain the interspecific divergence in flight morphology and echolocation vocalizations in some bat groups from the perspective of foraging ecology. However, the relationship between wing morphology and echolocation vocalizations of bats remains obscure, especially in a phylogenetic context.

Objectives

Here, we aimed to assess the correlated evolution of wing morphology and echolocation calls in bats within a phylogenetic comparative framework.

Methods

We integrated the information on search-phrase echolocation call duration, peak frequency, relative wing loading, aspect ratio, and foraging guilds for 152 bat species belonging to 15 families. We quantified the association among wing morphology, echolocation call parameters, and foraging guilds using phylogeny-based comparative analyses.

Results

Our analyses revealed that wing morphology and echolocation call parameters depended on families and exhibited a marked phylogenetic signal. Peak frequency of the call was negatively correlated with relative wing loading and aspect ratio. Call duration was positively correlated with relative wing loading and aspect ratio among open-space aerial foragers, edge-space aerial foragers, edge-space trawling foragers, and narrow-space gleaning foragers. Wing morphology, call duration, and peak frequency were predicted by foraging guilds.

Conclusion

These results demonstrate that adaptive response to foraging ecology has shaped the correlated evolution between flight morphology and echolocation calls in bats. Our findings expand the current knowledge regarding the link between morphology and vocalizations within the order Chiroptera.
Economic benefits of conservation biocontrol: A spatially explicit bioeconomic model for insect pest management in agricultural landscapes
Authors: Parry Hazel
Published: December 2022

Spatially explicit population dynamic models have been successfully used to explore management scenarios in terms of pest suppression across a wide range of systems. However, the economic implications of pest management, particularly in the case of biological control and non-crop management strategies, have not been well considered. A bioeconomic spatially explicit simulation model was developed, that integrates models of pest population dynamics, pest movement and economics of management. The utility of the model is demonstrated here usingNysius vinitor, a pest of grain crops in Australia. The model estimates the short- and long-term economic benefits of three pest management strategies: (1) in-field pesticide spray; (2) pest suppression through weed management in non-crop habitat; and (3) bolstering biocontrol through revegetation with, or maintenance of, native vegetation. Across all management types, high yield and low relative management cost resulted in a greater chance of a gross profit. The impacts of the pests themselves were shown to be non-linear, with an intermediate level of pest pressure maximizing the economic gain from management. Pest dispersal capacity influenced the profitability of management of non-crop vegetation, with lower pest dispersal resulting in a greater likelihood of benefit, as benefits from non-crop management are localized (e.g., increased beneficial insect populations). In an intensively cropped landscape, pesticide management was most profitable over the short-term. Once a 10-year horizon was reached, then the profitability of revegetation was greater and continued to increase. While weeding requirements are low, it is likely to always be profitable in the long-term to maintain or restore native vegetation in good condition to control this pest in an intensively cropped landscape. Using pesticide alongside revegetation gave some short-term gain, but the negative impact of pesticide on beneficials outweighed the benefit and in the long-term it is less profitable. These results do not hold in a low production landscape, due to increased pest pressure and costs of managing non-crop habitat. In summary, when quantified over a 10–20 year time horizon, revegetation or conserving native remnants in good (i.e., non-weedy) condition could be economically more beneficial to control an insect pest than ongoing pesticide use, in intensively cropped landscapes.
Single-cell RNA-seq data analysis using graph autoencoders and graph attention networks
Authors: Feng Xiang , Fang Fang , Long Haixia , Zeng Rao , Yao Yuhua
Published: December 2022

With the development of high-throughput sequencing technology, the scale of single-cell RNA sequencing (scRNA-seq) data has surged. Its data are typically high-dimensional, with high dropout noise and high sparsity. Therefore, gene imputation and cell clustering analysis of scRNA-seq data is increasingly important. Statistical or traditional machine learning methods are inefficient, and improved accuracy is needed. The methods based on deep learning cannot directly process non-Euclidean spatial data, such as cell diagrams. In this study, we developed scGAEGAT, a multi-modal model with graph autoencoders and graph attention networks for scRNA-seq analysis based on graph neural networks. Cosine similarity, median L1 distance, and root-mean-squared error were used to measure the gene imputation performance of different methods for comparison with scGAEGAT. Furthermore, adjusted mutual information, normalized mutual information, completeness score, and Silhouette coefficient score were used to measure the cell clustering performance of different methods for comparison with scGAEGAT. Experimental results demonstrated promising performance of the scGAEGAT model in gene imputation and cell clustering prediction on four scRNA-seq data sets with gold-standard cell labels.
Ferroptosis patterns and tumor microenvironment infiltration characterization in esophageal squamous cell cancer
Authors: Zhang Lu-Lu , Zhu Wei-Jie , Zhang Xin-Xin , Feng Da , Wang Xi-Cheng , Ding Ying , Wang Dong-Xia , Li Yi-Yang
Published: December 2022

Background: Esophageal Squamous Cell Cancer (ESCC) is an aggressive disease associated with a poor prognosis. As a newly defined form of regulated cell death, ferroptosis plays a crucial role in cancer development and treatment and might be a promising therapeutic target. However, the expression patterns of ferroptosis-related genes (FRGs) in ESCC remain to be systematically analyzed.

Methods: First, we retrieved the transcriptional profile of ESCC from TCGA and GEO datasets (GSE47404, GSE23400, and GSE53625) and performed unsupervised clustering to identify different ferroptosis patterns. Then, we used the ssGSEA algorithm to estimate the immune cell infiltration of these patterns and explored the differences in immune cell abundance. Common genes among patterns were finally identified as signature genes of ferroptosis patterns.

Results: Herein, we depicted the multi-omics landscape of FRGs through integrated bioinformatics analysis and identified three ESCC subtypes with distinct immune characteristics: clusters A-C. Cluster C was abundant in CD8+ T cells and other immune cell infiltration, while cluster A was immune-barren. By comparing the differently expressed genes between clusters of diverse datasets, we defined a gene signature for each cluster and successfully validated it in the TCGA-ESCC dataset.

Conclusion: We provided a comprehensive insight into the expression pattern of ferroptosis genes and their interaction with immune cell infiltration. Additionally, we established a gene signature to define the ferroptosis patterns, which might be used to predict the response to immunotherapy.
CLEC16A variants conferred a decreased risk to allergic rhinitis in the Chinese population
Authors: Niu Yongliang , Wang Haiying , Li Zhengqing , Shamsi Bilal Haider , Liu Mingxia , Liu Juan , Wang Qiang , Liu Yonglin
Published: December 2022

Background: Allergic rhinitis (AR) is a chronic respiratory disease. Hereditary factors played a key role in the pathogenesis of the AR. This study investigated the association between CLEC16A variants and AR risk in the Chinese population.

Methods: We applied Agena MassARRAY technology platform to genotype five single nucleotide polymorphisms (SNPs) located in CLEC16A in 1004 controls and 995 cases. The association between CLEC16A SNPs (rs2286973, rs887864, rs12935657, rs11645657 and rs36045143) and AR risk were calculated by logistic regression analysis, with odds ratio (OR) and 95% confidence interval (CI). False-positive report probability (FPRP) was also used to assess the significant results to reduce false positives. Multifactor dimensionality reduction (MDR) was completed to assess the interaction between CLEC16A variants to predict AR risk.

Results: Totally, CLEC16A (rs887864, rs12935657, rs2286973, rs11645657 and rs36045143) were significantly associated with AR risk. Therein, rs2286973, rs11645657 and rs36045143 were related to a decreased risk of AR in the people ≤ 43 years old, females and the people with BMI≤24, respectively. And rs887864 and rs12935657 were also associated with a decreased susceptibility of AR in the people >43 years old. Meanwhile, in the results of region stratification, rs887864 conferred a reduced risk to AR in the people from loess hilly area.

Conclusion:CLEC16A variants conferred a decreased risk to AR in the Chinese population.
Genomic adaptation of Ethiopian indigenous cattle to high altitude
Authors: Terefe Endashaw , Belay Gurja , Han Jianlin , Hanotte Olivier , Tijjani Abdulfatai
Published: December 2022

The mountainous areas of Ethiopia represent one of the most extreme environmental challenges in Africa faced by humans and other inhabitants. Selection for high-altitude adaptation is expected to have imprinted the genomes of livestock living in these areas. Here we assess the genomic signatures of positive selection for high altitude adaptation in three cattle populations from the Ethiopian mountainous areas (Semien, Choke, and Bale mountains) compared to three Ethiopian lowland cattle populations (Afar, Ogaden, and Boran), using whole-genome resequencing and three genome scan approaches for signature of selection (iHS, XP-CLR, and PBS). We identified several candidate selection signature regions and several high-altitude adaptation genes. These include genes such as ITPR2, MB, and ARNT previously reported in the human population inhabiting the Ethiopian highlands. Furthermore, we present evidence of strong selection and high divergence between Ethiopian high- and low-altitude cattle populations at three new candidate genes (CLCA2, SLC26A2, and CBFA2T3), putatively linked to high-altitude adaptation in cattle. Our findings provide possible examples of convergent selection between cattle and humans as well as unique African cattle signature to the challenges of living in the Ethiopian mountainous regions.
Identification of optimal reference genes for gene expression normalization in human osteosarcoma cell lines under proliferative conditions
Authors: Dong Xiaoming , Yang Qiwei , Du Zhenwu , Zhang Guizhen , Shi Chuankai , Qin Xuyuan , Song Yang
Published: December 2022

The molecular pathogenesis and therapeutic target research studies on osteosarcoma (OS) have developed well during the last few years using various OS cell lines with reverse transcription quantitative polymerase chain reaction (RT-qPCR). However, the identification of suitable reference genes of RT-qPCR for OS cell lines has not been reported. Here, we conducted the normalization research of 12 reference genes (GAPDH, ACTB, 18S, B2M, ALAS1, GUSB, HPRT1, HMBS, PPIA, PUM1, RPL29, and TBP) for gene expression analysis in four kinds of human OS cell lines (U2OS, Saos-2, HOS, and MG-63) to improve the investigation of molecular mechanisms and the accuracy of diagnosis and prognostic molecular targets of OS. The gene expression stability and applicability of the 12 reference gene candidates were determined using geNorm, NormFinder, and BestKeeper software. The results indicated that PUM1 and the combination of PPIA + ALAS1 were recommended as the optimal reference gene in these four different sources of human OS cell lines under proliferative conditions. The present study identified the most suitable reference genes and reference gene combinations for OS cell lines under proliferative conditions in order to use in gene expression profile analysis. A reliable standardized method has the potential to improve the understanding of the biological mechanisms underlying OS in the future.
HBD-2 variants and SARS-CoV-2: New insights into inter-individual susceptibility
Authors: Behairy Mohammed Y. , Soltan Mohamed A. , Eldeen Muhammad Alaa , Abdulhakim Jawaher A. , Alnoman Maryam M. , Abdel-Daim Mohamed M. , Otifi Hassan , Al-Qahtani Saleh M. , Zaki Mohamed Samir A. , Alsharif Ghadi , Albogami Sarah , Jafri Ibrahim , Fayad Eman , Darwish Khaled M. , Elhady Sameh S. , Eid Refaat A.
Published: December 2022

Background

A deep understanding of the causes of liability to SARS-CoV-2 is essential to develop new diagnostic tests and therapeutics against this serious virus in order to overcome this pandemic completely. In the light of the discovered role of antimicrobial peptides [such as human b-defensin-2 (hBD-2) and cathelicidin LL-37] in the defense against SARS-CoV-2, it became important to identify the damaging missense mutations in the genes of these molecules and study their role in the pathogenesis of COVID-19.

Methods

We conducted a comprehensive analysis with multiple in silico approaches to identify the damaging missense SNPs for hBD-2 and LL-37; moreover, we applied docking methods and molecular dynamics analysis to study the impact of the filtered mutations.

Results

The comprehensive analysis reveals the presence of three damaging SNPs in hBD-2; these SNPs were predicted to decrease the stability of hBD-2 with a damaging impact on hBD-2 structure as well. G51D and C53G mutations were located in highly conserved positions and were associated with differences in the secondary structures of hBD-2. Docking-coupled molecular dynamics simulation analysis revealed compromised binding affinity for hBD-2 SNPs towards the SARS-CoV-2 spike domain. Different protein–protein binding profiles for hBD-2 SNPs, in relation to their native form, were guided through residue-wise levels and differential adopted conformation/orientation.

Conclusions

The presented model paves the way for identifying patients prone to COVID-19 in a way that would guide the personalization of both the diagnostic and management protocols for this serious disease.
Potent immunomodulatory and antitumor effect of anti-CD20-IL2no-alpha tri-functional immunocytokine for cancer therapy
Authors: Casadesús Ana Victoria , Cruz Beatriz María , Díaz Wilden , González Miguel Ángel , Gómez Tania , Fernández Briandy , González Addys , Ledón Nuris , Sosa Katya , Castro Kathleen , López Armando , Plasencia Claudia , Ramírez Yaima , Teillaud Jean-Luc , Hernández Calixto , León Kalet , Hernández Tays
Published: December 2022

Introduction

The anti-CD20 antibody rituximab (RTX) has substantially improved outcomes of patients with B-cell lymphomas, although more efficient therapies are needed for refractory or relapsing lymphomas. An approach to increase the clinical effectiveness of anti-tumor therapy is the use of antibody-cytokine fusion proteins (immunocytokines (ICKs)) to deliver at the tumor site the antibody effector functions and cytokines that trigger anti-tumor activities. In particular, IL-2-based ICKs have shown significant results in preclinical studies but not in clinical trials due to the toxicity profile associated to high doses IL-2 and the undesired expansion of Tregs.

Methods

To improve the efficacy of RTX therapy, we fused a murine (mIgG2a) or a human (hIgG1) version of RTX to a mutated IL-2 (no-alpha mutein), which has a disrupted affinity for the high affinity IL-2 receptor (IL-2R) to prevent the stimulation of Tregs and reduce the binding to endothelial cells expressing CD25, the α chain of high affinity IL-2R. Characterization of anti-CD20-IL2no-alpha ICKs was performed by SDS-PAGE, Western-blotting and SEC-HPLC and also by several functional in vitro techniques like T-cell proliferation assays, apoptosis, CDC and ADCC assays. The in vivo activity was assessed by using murine tumor cells expressing huCD20 in C57/Bl6 mice.

Results

Both ICKs exhibited similar in vitro specific activity of their IL2no-alpha mutein moieties and kept CD20-binding capacity. Anti-CD20-IL2no-alpha (hIgG1) retained antibody effector functions as complement-dependent cytotoxicity and enhanced direct apoptosis, NK cell activation and antibody-dependent cellular cytotoxicity relative to RTX. In addition, both ICKs demonstrated a higher antitumor efficacy than parental molecules or their combination in an EL4-huCD20 tumor model in immunocompetent mice. Anti-CD20-IL2no-alpha (hIgG1) strongly expanded NK and CD8+ T cells but not Tregs in tumor-bearing mice.

Discussion

These findings suggest that anti-CD20-IL2no-alpha could represent an alternative treatment for B cell lymphoma patients, mainly those refractory to RTX therapy.
Nanomaterials targeting macrophages in sepsis: A promising approach for sepsis management
Authors: Song Chaoying , Xu Jiqian , Gao Chenggang , Zhang Wanying , Fang Xiangzhi , Shang You
Published: December 2022

Sepsis is a life-threatening organ dysfunction resulting from dysregulated host responses to infection. Macrophages play significant roles in host against pathogens and the immunopathogenesis of sepsis, such as phagocytosis of pathogens, secretion of cytokines, and phenotype reprogramming. However, the rapid progression of sepsis impairs macrophage function, and conventional antimicrobial and supportive treatment are not sufficient to restore dysregulated macrophages roles. Nanoparticles own unique physicochemical properties, surface functions, localized surface plasmon resonance phenomenon, passive targeting in vivo, good biocompatibility and biodegradability, are accessible for biomedical applications. Once into the body, NPs are recognized by host immune system. Macrophages are phagocytes in innate immunity dedicated to the recognition of foreign substances, including nanoparticles, with which an immune response subsequently occurs. Various design strategies, such as surface functionalization, have been implemented to manipulate the recognition of nanoparticles by monocytes/macrophages, and engulfed by them to regulate their function in sepsis, compensating for the shortcomings of sepsis traditional methods. The review summarizes the mechanism of nanomaterials targeting macrophages and recent advances in nanomedicine targeting macrophages in sepsis, which provides good insight for exploring macrophage-based nano-management in sepsis.
Repurposing BCL-2 and Jak 1/2 inhibitors: Cure and treatment of HIV-1 and other viral infections
Authors: Reece Monica D. , Song Colin , Hancock Sarah C. , Pereira Ribeiro Susan , Kulpa Deanna A. , Gavegnano Christina
Published: December 2022

B cell lymphoma 2 (BCL-2) family proteins are involved in the mitochondrial apoptotic pathway and are key modulators of cellular lifespan, which is dysregulated during human immunodeficiency virus type 1 (HIV-1) and other viral infections, thereby increasing the lifespan of cells harboring virus, including the latent HIV-1 reservoir. Long-lived cells harboring integrated HIV-1 DNA is a major barrier to eradication. Strategies reducing the lifespan of reservoir cells could significantly impact the field of cure research, while also providing insight into immunomodulatory strategies that can crosstalk to other viral infections. Venetoclax is a first-in-class orally bioavailable BCL-2 homology 3 (BH3) mimetic that recently received Food and Drug Administration (FDA) approval for treatment in myeloid and lymphocytic leukemia. Venetoclax has been recently investigated in HIV-1 and demonstrated anti-HIV-1 effects including a reduction in reservoir size. Another immunomodulatory strategy towards reduction in the lifespan of the reservoir is Jak 1/2 inhibition. The Jak STAT pathway has been implicated in BCL-2 and interleukin 10 (IL-10) expression, leading to a downstream effect of cellular senescence. Ruxolitinib and baricitinib are FDA-approved, orally bioavailable Jak 1/2 inhibitors that have been shown to indirectly decay the HIV-1 latent reservoir, and down-regulate markers of HIV-1 persistence, immune dysregulation and reservoir lifespan in vitro and ex vivo. Ruxolitinib recently demonstrated a significant decrease in BCL-2 expression in a human study of virally suppressed people living with HIV (PWH), and baricitinib recently received emergency use approval for the indication of coronavirus disease 2019 (COVID-19), underscoring their safety and efficacy in the viral infection setting. BCL-2 and Jak 1/2 inhibitors could be repurposed as immunomodulators for not only HIV-1 and COVID-19, but other viruses that upregulate BCL-2 anti-apoptotic proteins. This review examines potential routes for BCL-2 and Jak 1/2 inhibitors as immunomodulators for treatment and cure of HIV-1 and other viral infections.
Pyruvate: Ferredoxin oxidoreductase is involved in IgA-related microbiota dysbiosis and intestinal inflammation
Authors: Wang Kairuo , Guo Yixuan , Liu Yuanyuan , Cui Xiao , Gu Xiang , Li Lixiang , Li Yanqing , Li Ming
Published: December 2022

Introduction

Inflammatory bowel diseases (IBDs) are associated with both immune abnormalities and dysbiosis, characterized by a loss of Faecalibacterium prausnitzii (F. prausnitzii). However, the reason for F. prausnitzii deficiency remains unclear.

Methods

16S rDNA seque­ncing and IgA enzyme-linked immunosorbent assay (ELISA) were applied to identify bacterial community and IgA changes in ulcerative colitis (UC) patients. Forced immunization with F. prausnitzii in rabbits was conducted. To screen for potential IgA-reactive proteins in F. prausnitzii lysates, we performed western blotting and mass spectrometry analyses. Pyruvate: ferredoxin oxidoreductase (PFOR) was cloned and purified, then the immunoreactivity of PFOR was verified in peripheral blood mononuclear cells (PBMCs) through PCR, ELISpot assay and single-cell sequencing (scRNA-seq). Finally, the UC fecal dysbiosis was re-analyzed in the context of the phylogenetic tree of PFOR.

Results

F. prausnitzii was underrepresented in UC patients with elevated F. prausnitzii-reactive IgA in the fecal supernatant. Forced immunization with F. prausnitzii in rabbits led to high interferon-γ (IFN-γ) transcription in the colon, along with beta diversity disturbance and intestinal inflammation. PFOR was identified as an IgA-binding antigen of F. prausnitzii and the immunoreactivity was validated in PBMCs, which showed elevated expression of inflammatory cytokines. The scRNA-seq revealed enhanced signals in both T regulatory cells (Tregs) and monocytes after PFOR incubation. Furthermore, phylogenetic analysis revealed that PFOR was a common but conserved protein among the gut bacteria.

Discussion

Our results collectively suggest that PFOR is a bioactive protein in the immune system and may contribute to host-microbial crosstalk. Conserved but bioactive microbial proteins, such as PFOR, warrant more attention in future host-microbial interaction studies.
Case report: Nocardia gipuzkoensis infection in an immunocompetent patient diagnosed by metagenomic next-generation sequencing and whole genome sequencing
Authors: Liu Chengxin , Yang Juhua , Huang Huiting , Zhan Shaofeng , Xia Xintian
Published: December 2022

The infection of Nocardia gipuzkoensis is a relatively uncommon form of pulmonary nocardiosis seen in clinical patients. In general, nocardiosis tends to occur in patients with immune deficiency. Here, we report a 23-year-old female who was admitted to the hospital due to cough and sputum production over 10 years, diagnosed with bronchiectasis. The N. gipuzkoensis infection was identified by metagenomic next-generation sequencing and whole genome sequencing. Imipenem/cilastatin and compound sulfamethoxazole tablets were used to control the infection and the pulmonary inflammation subsided gradually.
Donor chimerism and immune reconstitution following haploidentical transplantation in sickle cell disease
Authors: Chu Yaya , Talano Julie-An , Baxter-Lowe Lee Ann , Verbsky James W. , Morris Erin , Mahanti Harshini , Ayello Janet , Keever-Taylor Carolyn , Johnson Bryon , Weinberg Rona S. , Shi Qiuhu , Moore Theodore B. , Fabricatore Sandra , Grossman Brenda , van de Ven Carmella , Shenoy Shalini , Cairo Mitchell S.
Published: December 2022

Introduction

We previously reported the initial results of a phase II multicenter transplant trial using haploidentical parental donors for children and aolescents with high-risk sickle cell disease achieving excellent survival with exceptionally low rates of graft-versus-host disease and resolution of sickle cell disease symptoms. To investigate human leukocyte antigen (HLA) sensitization, graft characteristics, donor chimerism, and immune reconstitution in these recipients.

Methods

CD34 cells were enriched using the CliniMACS® system with a target dose of 10 x 106 CD34+ cells/kg with a peripheral blood mononuclear cell (PBMNC) addback dose of 2x105 CD3/kg in the final product. Pre-transplant HLA antibodies were characterized. Donor chimerism was monitored 1-24 months post-transplant. Comprehensive assessment of immune reconstitution included lymphocyte subsets, plasma cytokines, complement levels, anti-viral T-cell responses, activation markers, and cytokine production. Infections were monitored.

Results

HLA antibodies were detected in 7 of 11 (64%) evaluable patients but rarely were against donor antigens. Myeloid engraftment was rapid (100%) at a median of 9 days. At 30 days, donor chimerism was 93-99% and natural killer cell levels were restored. By 60 days, CD19 B cells were normal. CD8 and CD4 T-cells levels were normal by 279 and 365 days, respectively. Activated CD4 and CD8 T-cells were elevated at 100-365 days post-transplant while naïve cells remained below baseline. Tregs were elevated at 100-270 days post-transplant, returning to baseline levels at one year. At one year, C3 and C4 levels were above baseline and CH50 levels were near baseline. At one year, cytokine levels were not significantly different from baseline.

Discussion

These results suggest that haploidentical transplantation with CD34-enriched cells and peripheral blood mononuclear cell addback results in rapid engraftment, sustained donor chimerism and broad-based immune reconstitution.
Changes in humpback whale song structure and complexity reveal a rapid evolution on a feeding ground in Northern Norway
Authors: Tyarks Saskia C. , Aniceto Ana S. , Ahonen Heidi , Pedersen Geir , Lindstrøm Ulf
Published: December 2022

Singing behaviour by male humpback whales (Megaptera novaeangliae) has traditionally been associated with low-latitude breeding grounds. However, in recent years, this vocal behaviour has been increasingly reported outside these areas. All singers in a given population sing the same version of a song and this song is continually evolving over time with modifications on different levels within the song structure. Tracing changes in whale song will help to undercover the drivers underlying this vocal display and contribute to the understanding of animal culture and its evolution. To determine the progressive changes in songs found on a subarctic feeding ground and migratory stopover, a detailed analysis of humpback whale song recordings from Northern Norway was conducted. Passive acoustic data from the Lofoten-Vesterålen Ocean Observatory (LoVe), collected using a bottom-moored underwater hydrophone, were used from January - April 2018 and January 2019. Two measures of the song structure were examined: (1) sequence similarities using the Levenshtein distance and (2) song complexity using a principal component analysis (PCA). In total, 21 distinct themes were identified which presented highly directional, structural changes over time. Two themes from 2018 reoccurred in 2019, whereas all other themes in 2019 appeared to be evolved versions of 2018 themes. All songs grouped into three general clusters, reflecting the rapid evolution over the study period. With all sampled animals singing the same version of the song, this might indicate that the singers are either from the same breeding population or that song learning occurred before the study period. Song complexity appeared to follow the trend of song progression; songs became more complex as they evolved over the months in 2018 and decreased in complexity between the years, returning to a more simplified song in 2019. The results confirm that humpback whale song exhibits a rapid progression on a shared subarctic feeding ground, with strong potential for song exchange and opportunities for cultural transmission between populations in the North Atlantic.
The impact of Helicobacter pylori and intestinal helminth infections on gastric adenocarcinoma and inflammatory bowel disease in Sub-Saharan Africa
Authors: Setshedi Mashiko , Watermeyer Gillian
Published: December 2022

Gastric adenocarcinoma (GCA) is the 5th leading cancer globally with an estimated 1.1 million cases reported in 2020. Ninety percent of non-cardia GCAs are attributable to Helicobacter pylori (H. pylori), the most prevalent bacterial infection globally. Rates of H. pylori infection are highest in Sub-Saharan Africa (SSA), yet surprisingly low numbers of GCAs are reported in the region. A similar phenomenon is seen with the inflammatory bowel diseases (IBD), Crohn’s disease, and ulcerative colitis. These disorders have risen dramatically over the past century in high income countries across the globe, with sharp increases noted more recently in newly industrialized regions. In contrast IBD is rare in most regions in SSA. For both diseases this may reflect under-reporting or limited access to diagnostic modalities, but an alternative explanation is the high burden of infection with gastrointestinal parasites endemic to SSA which may attenuate the risk of developing GCA and IBD. In this mini review we discuss the complex interplay between these microorganisms, GCA, and IBD, as well as a possible protective role of H. pylori and the development of IBD.
Prognosis prediction performs better in patients with non-cirrhosis hepatitis B virus-related acute-on-chronic liver failure than those with cirrhosis
Authors: Yu Xia , Li Hai , Tan Wenting , Wang Xianbo , Zheng Xin , Huang Yan , Li Beiling , Meng Zhongji , Gao Yanhang , Qian Zhiping , Liu Feng , Lu Xiaobo , Shang Jia , Yan Huadong , Zheng Yubao , Zhang Weituo , Yin Shan , Gu Wenyi , Deng Guohong , Xiang Xiaomei , Zhou Yi , Hou Yixin , Zhang Qun , Xiong Shue , Liu Jing , Chen Ruochan , Long Liyuan , Chen Jinjun , Jiang Xiuhua , Luo Sen , Chen Yuanyuan , Jiang Chang , Zhao Jinming , Ji Liujuan , Mei Xue , Li Jing , Li Tao , Zheng Rongjiong , Zhou Xinyi , Ren Haotang , Sheng Jifang , Shi Yu
Published: December 2022

Background

The accurate prediction of the outcome of hepatitis B virus-related acute-on-chronic liver failure (HBV-ACLF) is impeded by population heterogeneity. The study aimed to assess the impact of underlying cirrhosis on the performance of clinical prediction models (CPMs).

Methods

Using data from two multicenter, prospective cohorts of patients with HBV-ACLF, the discrimination, calibration, and clinical benefit were assessed for CPMs predicting 28-day and 90-day outcomes in patients with cirrhosis and those without, respectively.

Results

A total of 919 patients with HBV-ACLF were identified by Chinese Group on the Study of Severe Hepatitis B (COSSH) criteria, including 675 with cirrhosis and 244 without. COSSH-ACLF IIs, COSSH-ACLFs, Chronic Liver Failure-Consortium Acute-on-Chronic Liver Failure score (CLIF-C ACLFs), Tongji Prognostic Predictor Model score (TPPMs), Model for End-Stage Liver Disease score (MELDs), and MELD-Sodium score (MELD-Nas) were all strong predictors of short-term mortality in patients with HBV-ACLF. In contrast to a high model discriminative capacity in ACLF without cirrhosis, each prognostic model represents a marked decline of C-index, net reclassification index (NRI), and integrated discrimination improvement (IDI) in predicting either 28-day or 90-day prognosis of patients with cirrhosis. The hazard analysis identified largely overlapping risk factors of poor outcomes in both subgroups, while serum bilirubin was specifically associated with short-term mortality in patients with cirrhosis and blood urea nitrogen in patients without cirrhosis. A subgroup analysis in patients with cirrhosis showed a decline of discrimination of CPMS in those with ascites or infections compared to that in those without.

Conclusion

Predicting the short-term outcome of HBV-ACLF by CPMs is optimal in patients without cirrhosis but limited in those with cirrhosis, at least partially due to the complicated ascites or infections.
Children gut microbiota exhibits a different composition and metabolic profile after in vitro exposure to Clostridioides difficile and increases its sporulation
Authors: Horvat Sabina , Mahnic Aleksander , Makuc Damjan , Pečnik Klemen , Plavec Janez , Rupnik Maja
Published: December 2022

Clostridioides difficile (Clostridium difficile) infection (CDI) is one of the main public health concerns in adults, while children under 2 years of age are often colonized asymptomatically. In both adults and children, CDI is strongly associated with disturbances in gut microbiota. In this study, an in-vitro model of children gut microbiota was challenged with vegetative cells or a conditioned media of six different toxigenic C. difficile strains belonging to the ribotypes 027, 078, and 176. In the presence of C. difficile or conditioned medium the children gut microbiota diversity decreased and all main phyla (Bacteroidetes, Firmicutes, and Proteobacteria) were affected. The NMR metabolic spectra divided C. difficile exposed children gut microbiota into three clusters. The grouping correlated with nine metabolites (short chain fatty acids, ethanol, phenolic acids and tyramine). All strains were able to grow in the presence of children gut microbiota and showed a high sporulation rate of up to 57%. This high sporulation rate in combination with high asymptomatic carriage in children could contribute to the understanding of the reported role of children in C. difficile transmissions.
Changes in gut microbiota and metabolism associated with phenotypic plasticity in the honey bee Apis mellifera
Authors: Copeland Duan C. , Maes Patrick W. , Mott Brendon M. , Anderson Kirk E.
Published: December 2022

Honey bees exhibit an elaborate social structure based in part on an age-related division of labor. Young workers perform tasks inside the hive, while older workers forage outside the hive, tasks associated with distinct diets and metabolism. Critical to colony fitness, the work force can respond rapidly to changes in the environment or colony demography and assume emergency tasks, resulting in young foragers or old nurses. We hypothesized that both task and age affect the gut microbiota consistent with changes to host diet and physiology. We performed two experiments inducing precocious foragers and reverted nurses, then quantified tissue-specific gut microbiota and host metabolic state associated with nutrition, immunity and oxidative stress. In the precocious forager experiment, both age and ontogeny explained differences in midgut and ileum microbiota, but host gene expression was best explained by an interaction of these factors. Precocious foragers were nutritionally deficient, and incurred higher levels of oxidative damage relative to age-matched nurses. In the oldest workers, reverted nurses, the oxidative damage associated with age and past foraging was compensated by high Vitellogenin expression, which exceeded that of young nurses. Host-microbial interactions were evident throughout the dataset, highlighted by an age-based increase of Gilliamella abundance and diversity concurrent with increased carbonyl accumulation and CuZnSOD expression. The results in general contribute to an understanding of ecological succession of the worker gut microbiota, defining the species-level transition from nurse to forager.
Survival of a surrogate African swine fever virus-like algal virus in feed matrices using a 23-day commercial United States truck transport model
Authors: Palowski Amanda , Balestreri Cecilia , Urriola Pedro E. , van de Ligt Jennifer L. G. , Sampedro Fernando , Dee Scott , Shah Apoorva , Yancy Haile F. , Shurson Gerald C. , Schroeder Declan C.
Published: December 2022

African swine fever virus (ASFV) is a member of the nucleocytoplasmic large DNA viruses (NCLDVs) and is stable in a variety of environments, including animal feed ingredients as shown in previous laboratory experiments and simulations. Emiliania huxleyi virus (EhV) is another member of the NCLDVs, which has a restricted host range limited to a species of marine algae called Emiliania huxleyi. This algal NCLDV has many similar morphological and physical characteristics to ASFV thereby making it a safe surrogate, with results that are applicable to ASFV and suitable for use in real-world experiments. Here we inoculated conventional soybean meal (SBMC), organic soybean meal (SBMO), and swine complete feed (CF) matrices with EhV strain 86 (EhV-86) at a concentration of 6.6 × 107 virus g−1, and then transported these samples in the trailer of a commercial transport vehicle for 23 days across 10,183 km covering 29 states in various regions of the United States. Upon return, samples were evaluated for virus presence and viability using a previously validated viability qPCR (V-qPCR) method. Results showed that EhV-86 was detected in all matrices and no degradation in EhV-86 viability was observed after the 23-day transportation event. Additionally, sampling sensitivity (we recorded unexpected increases, as high as 49% in one matrix, when virus was recovered at the end of the sampling period) rather than virus degradation best explains the variation of virus quantity observed after the 23-day transport simulation. These results demonstrate for the first time that ASFV-like NCLDVs can retain viability in swine feed matrices during long-term transport across the continental United States.
Fifty-year habitat subdivision enhances soil microbial biomass and diversity across subtropical land-bridge islands
Authors: Wu Ying , Wang Bing , Wu Liji , Liu Shengen , Yue Lingyan , Wu Jianping , Chen Dima
Published: December 2022

Although habitat loss and subdivision are considered main causes of sharp declines in biodiversity, there is still great uncertainty concerning the response of soil microbial biomass, diversity, and assemblage to habitat subdivision at the regional scale. Here, we selected 61 subtropical land-bridge islands (with small, medium, and large land areas) with a 50-year history of habitat subdivision and 9 adjacent mainland sites to investigate how habitat subdivision-induced unequal-sized patches and isolation affects biomass, diversity, and assemblages of soil bacteria and fungi. We found that the soil bacterial and fungal biomass on all unequal-sized islands were higher than that on mainland, while soil bacterial and fungal richness on the medium-sized islands were higher than that on mainland and other-sized islands. The habitat subdivision-induced increases in microbial biomass or richness were mainly associated with the changes in subdivision-specified habitat heterogeneities, especial for soil pH and soil moisture. Habitat subdivision reduced soil bacterial dissimilarity on medium-sized islands but did not affect soil fungal dissimilarity on islands of any size. The habitat fragment-induced changes in soil microbial dissimilarity were mainly associated with microbial richness. In summary, our results based on the responses of soil microbial communities from subtropical land-bridge islands are not consistent with the island biogeographical hypotheses but are to some extent consistent with the tradeoff between competition and dispersal. These findings indicate that the response of soil microbial communities to habitat subdivision differed by degree of subdivision and strongly related to habitat heterogeneity, and the distribution of microbial diversity among islands is also affected by tradeoff between competition and dispersal.
Associations of audiometric hearing and speech-in-noise performance with cognitive decline among older adults: The Baltimore Longitudinal Study of Aging (BLSA)
Authors: Jiang Kening , Armstrong Nicole M. , Agrawal Yuri , Gross Alden L. , Schrack Jennifer A. , Lin Frank R. , Ferrucci Luigi , Resnick Susan M. , Deal Jennifer A. , Powell Danielle S.
Published: December 2022

Background

Established associations between hearing loss and cognitive decline were primarily defined by pure-tone audiometry, which reflects peripheral hearing ability. Speech-in-noise performance, which reflects central hearing ability, is more limited in prior literature. We examined the longitudinal associations of audiometric hearing and speech-in-noise performance with cognitive decline.

Methods

We studied 702 participants aged ≥60 years in the Baltimore Longitudinal Study of Aging 2012–2019. Global and domain-specific (language, memory, attention, executive function, visuospatial ability) cognitive performance were assessed by the cognitive assessment battery. Hearing thresholds at 0.5, 1, 2, and 4 kilohertz obtained from pure-tone audiometry were averaged to calculate better-ear pure-tone average (PTA) and participants were categorized as having hearing loss (>25 decibels hearing level [dB HL]) or normal hearing (≤25 dB HL). Speech-in-noise performance was assessed by the Quick Speech-in-Noise (QuickSIN) test, and participants were categorized as having below-median (worse) or above-median performance. Linear mixed effects models with random intercepts and slopes were used to assess baseline cognitive performance and cognitive decline by hearing status. Models adjusted for demographic, lifestyle and disease factors.

Results

Participants with audiometric hearing loss showed similar baseline cognitive performance but faster decline in global cognitive function, language, executive function, and attention. Participants with below-median QuickSIN score showed worse baseline cognitive performance in all domains and faster decline in global cognitive function, language, memory, executive function and attention.

Conclusions

Audiometric hearing might be targeted to delay cognitive decline. Speech-in-noise performance might be a novel marker and might be more sensitive to memory decline.
Determinants of early working impairments in multiple sclerosis
Authors: Moccia Marcello , Fontana Luca , Palladino Raffaele , Falco Fabrizia , Finiello Ferdinando , Fedele Mauro , Lanzillo Roberta , Reppuccia Liberata , Triassi Maria , Brescia Morra Vincenzo , Iavicoli Ivo
Published: December 2022

Introduction

Unemployment can directly affect social status and identity. Assessing and adjusting determinants of early working impairments in a chronic disease can thus reduce its long-term burden. Hereby, we aim to evaluate differences in occupational history and early working impairments between people with multiple sclerosis (MS) and healthy workers.

Methods

This is a cross-sectional study comparing 71 workers with MS [age 41.7 ± 9.4 years; females 59.1%; EDSS 2.0 (1.0–6.0)] and 71 controls (age 42.6 ± 11.9 years; females 33.8%). All participants filled in Work Ability Index (WAI), Work Productivity and Activity Impairment (WPAI), European Questionnaire for Quality of Life (EuroQoL), Beck Depression Inventory II (BDI-II), and Pittsburgh Sleep Quality Index (PSQI). In MS, we further collected expanded disability status scale (EDSS), MS Questionnaire for Job difficulties (MSQ-Job), Fatigue severity scale (FSS), and the Brief International Cognitive Assessment for MS (BICAMS).

Results

Workers with MS were more working disabled (p < 0.01), less exposed to workplace risks (p < 0.01), and more limited in fitness to work (p = 0.01), compared with controls. On linear regression models adjusted by age, sex, education, and type of contract, people with MS had worse WAI (Coeff=−5.47; 95% CI = −7.41, −3.53; p < 0.01), EuroQoL (Coeff = −4.24; 95% CI = −17.85, −6.50; p < 0.01), BDI-II (Coeff = 3.99; 95% CI = 2.37, 7.01; p < 0.01), and PSQI (Coeff = 4.74; 95% CI = 3.13, 7.61; p < 0.01), compared with controls, but no differences in WPAI (p = 0.60). EuroQoL, BDI-II, and PSQI were equally associated with both WAI and WPAI in MS and controls (all p< 0.01). In MS, worse MSQJob was associated with higher EDSS (Coeff = 5.22; 95% CI = 2.24, 7.95; p < 0.01), progressive disease (Coeff = 14.62; 95% CI = 5.56, 23.69; p < 0.01), EuroQoL (Coeff = 4.63; 95% CI = 2.92, 6.35; p < 0.01), FSS (Coeff = 0.55; 95% CI = 0.38, 0.72; p < 0.01), and cognitive impairment (Coeff = 4.42; 95% CI = 0.67, 8.22; p = 0.02).

Discussion

Early factors associated with working difficulties in MS include disability, fatigue, depression, and cognitive dysfunction. Early identification of clinical features potentially causing working difficulties should be considered to enhance job retention, along with targeted prevention and protection measures.
How far is brain-inspired artificial intelligence away from brain?
Authors: Chen Yucan , Wei Zhengde , Gou Huixing , Liu Haiyi , Gao Li , He Xiaosong , Zhang Xiaochu
Published: December 2022

Fueled by the development of neuroscience and artificial intelligence (AI), recent advances in the brain-inspired AI have manifested a tipping-point in the collaboration of the two fields. AI began with the inspiration of neuroscience, but has evolved to achieve a remarkable performance with little dependence upon neuroscience. However, in a recent collaboration, research into neurobiological explainability of AI models found that these highly accurate models may resemble the neurobiological representation of the same computational processes in the brain, although these models have been developed in the absence of such neuroscientific references. In this perspective, we review the cooperation and separation between neuroscience and AI, and emphasize on the current advance, that is, a new cooperation, the neurobiological explainability of AI. Under the intertwined development of the two fields, we propose a practical framework to evaluate the brain-likeness of AI models, paving the way for their further improvements.