bluuebunny/crossref_metadata_2025 huggingface dataset:
Immunogenic self-peptides - the great unknowns in autoimmunity: Identifying T-cell epitopes driving the autoimmune response in autoimmune diseases
Authors: Prinz Jörg Christoph
Published: January 2023

HLA-associated autoimmune diseases likely arise from T-cell-mediated autoimmune responses against certain self-peptides from the broad HLA-presented immunopeptidomes. The limited knowledge of the autoimmune target peptides has so far compromised the basic understanding of autoimmune pathogenesis. This is due to the complexity of antigen processing and presentation as well as the polyspecificity of T-cell receptors (TCRs), which pose high methodological challenges on the discovery of immunogenic self-peptides. HLA-class I molecules present peptides to CD8+ T cells primarily derived from cytoplasmic proteins. Therefore, HLA-class I-restricted autoimmune responses should be directed against target cells expressing the corresponding parental protein. In HLA-class II-associated diseases, the origin of immunogenic peptides is not pre-specified, because peptides presented by HLA-class II molecules to CD4+ T cells may originate from both extracellular and cellular self-proteins. The different origins of HLA-class I and class II presented peptides determine the respective strategy for the discovery of immunogenic self-peptides in approaches based on the TCRs isolated from clonally expanded pathogenic T cells. Both involve identifying the respective restricting HLA allele as well as determining the recognition motif of the TCR under investigation by peptide library screening, which is required to search for homologous immunogenic self-peptides. In HLA-class I-associated autoimmune diseases, identification of the target cells allows for defining the restricting HLA allotype from the 6 different HLA-class I alleles of the individual HLA haplotype. It furthermore limits the search for immunogenic self-peptides to the transcriptome or immunopeptidome of the target cells, although neoepitopes generated by peptide splicing or translational errors may complicate identification. In HLA class II-associated autoimmune diseases, the lack of a defined target cell and differential antigen processing in different antigen-presenting cells complicate identification of the HLA restriction of autoreactive TCRs from CD4+ T cells. To avoid that all corresponding HLA-class II allotypes have to be included in the peptide discovery, autoantigens defined by autoantibodies can guide the search for immunogenic self-peptides presented by the respective HLA-class II risk allele. The objective of this article is to highlight important aspects to be considered in the discovery of immunogenic self-peptides in autoimmune diseases.
A highly efficient indirect ELISA and monoclonal antibody established against African swine fever virus pK205R
Authors: Li Liwei , Qiao Sina , Liu Jiachen , Zhou Yanjun , Tong Wu , Dong Shishan , Liu Changlong , Jiang Yifeng , Guo Ziqiang , Zheng Haihong , Zhao Ran , Tong Guangzhi , Li Guoxin , Gao Fei
Published: January 2023

African swine fever (ASF) is a contagious infectious disease with high lethality which continuously threatens the global pig industry causing huge economic losses. Currently, there are no commercially available vaccines or antiviral drugs that can effectively control ASF. The pathogen of ASF, ASF virus (ASFV) is a double-stranded DNA virus with a genome ranging from 170 to 193 kb and 151 to 167 open reading frames in various strains, which encodes 150–200 proteins. An effective method of monitoring ASFV antibodies, and specific antibodies against ASFV to promote the development of prevention techniques are urgently needed. In the present study, pK205R of ASFV was successfully expressed in mammalian cells using a suspension culture system. An indirect enzyme-linked immunosorbent assay (ELISA) based on the purified pK205R was established and optimized. The monoclonal antibody (mAb) against pK205R recognized a conservative linear epitope (2VEPREQFFQDLLSAV16) and exhibited specific reactivity, which was conducive to the identification of the recombinant porcine reproductive and respiratory syndrome virus (PRRSV) expressing pK205R. The ELISA method efficiently detected clinical ASFV infection and revealed good application prospects in monitoring the antibody level in vivo for recombinant PRRSV live vector virus expressing the ASFV antigen protein. The determination of the conserved linear epitope of pK205R would contribute to further research on the structural biology and function of pK205R. The indirect ELISA method and mAb against ASFV pK205R revealed efficient detection and promising application prospects, making them ideal for epidemiological surveillance and vaccine research on ASF.
Cannabinoid receptor 2 plays a pro-tumorigenic role in non-small cell lung cancer by limiting anti-tumor activity of CD8+ T and NK cells
Authors: Sarsembayeva Arailym , Kienzl Melanie , Gruden Eva , Ristic Dusica , Maitz Kathrin , Valadez-Cosmes Paulina , Santiso Ana , Hasenoehrl Carina , Brcic Luka , Lindenmann Jörg , Kargl Julia , Schicho Rudolf
Published: January 2023

Cannabinoid (CB) receptors (CB1and CB2) are expressed on cancer cells and their expression influences carcinogenesis in various tumor entities. Cells of the tumor microenvironment (TME) also express CB receptors, however, their role in tumor development is still unclear. We, therefore, investigated the role of TME-derived CB1and CB2receptors in a model of non-small cell lung cancer (NSCLC). Leukocytes in the TME of mouse and human NSCLC express CB receptors, with CB2showing higher expression than CB1. In the tumor model, using CB1- (CB1-/-) and CB2-knockout (CB2-/-) mice, only deficiency of CB2, but not of CB1, resulted in reduction of tumor burden vs. wild type (WT) littermates. This was accompanied by increased accumulation and tumoricidal activity of CD8+T and natural killer cells, as well as increased expression of programmed death-1 (PD-1) and its ligand on lymphoid and myeloid cells, respectively. CB2-/-mice responded significantly better to anti-PD-1 therapy than WT mice. The treatment further increased infiltration of cytotoxic lymphocytes into the TME of CB2-/-mice. Our findings demonstrate that TME-derived CB2dictates the immune cell recruitment into tumors and the responsiveness to anti-PD-1 therapy in a model of NSCLC. CB2could serve as an adjuvant target for immunotherapy.
Transcriptomic profile of symbiotic accessory nidamental gland during female maturation in bigfin reef squid
Authors: Tseng Peng-Wei , Li Hau-Wen , Chen Chih , Tseng Yung-Che , Chang Ching-Fong , Wu Guan-Chung
Published: January 2023

The bigfin reef squid, Sepioteuthis lessoniana, are a valuable commercial species in East Asian regions such as Taiwan and Japan. A lack of genomic information limits the application of potential aquaculture techniques, especially in breeding when considering the hatching rate of offspring. In some squids and cuttlefishes, symbiotic bacteria are transmitted from the accessory nidamental gland (ANG) to the jelly coat of eggs. In Hawaiian bobtail squid, these parent-delivered mutualistic bacteria play an important role in preventing lethal biofouling of the eggs and accelerating the hatch rate of offspring. The bacterial consortium, which is housed in the female squids ANG, are governed by host selection during female maturation. Immune functions are typically used to explain the regulatory mechanism of symbioses by host selection. In this study, we evaluated the transcripts featured in bacterial selection and maintenance during ANG development using RNA-seq. Different developmental stages of ANGs (stages 1–4) were sequenced. The de novo transcriptome assembly resulted in 524,918 unigenes. Two groups, non-pigmentation group (stage 1 and stage 3) and pigmentation group (stage 4), were clustered by transcriptome-wide expression profile analysis. The gene expression analyses indicated that 9,475 differential expression genes (DEGs) in three different phases and 1,363 (14.3%) DEGs were matched in the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. Furthermore, KEGG-enriched analysis results suggested that immune responses are a dominant pathway in the non-pigmentation group (stage 1 and stage 3) whereas lipid metabolism and metabolism of flora fermentation are dominant in the pigmentation group (stage 4). Although the host immunity plays an important role during bacterial colonization of the ANG in bigfin reef squid, our results showed that most immune-related genes had a reduced transcriptomic level in the pigmentation group compared with the non-pigmentation group. Therefore, our results provide new insight to understand the regulatory mechanisms of initial bacterial colonization and later bacterial pigmentation in the bigfin reef squid.
Transport inventories and exchanges of organic matter throughout the St. Lawrence Estuary continuum (Canada)
Authors: Lévesque David , Lebeuf Michel , Maltais Domynick , Anderson Caroline , Starr Michel
Published: January 2023

Hypoxia (O2 < 2 mg/L) driven by eutrophication in estuaries and shelves is a worldwide expanding problem. The role of organic matter (OM) inputs is emerging as an important contributor to this issue, beside the well-known implication of inorganic nutrients. The St. Lawrence Estuary, one of the largest and deepest estuarine system in the world is facing strong persistent and increasing hypoxia. In this context, transport and exchange of particulate and dissolved organic matter (POM and DOM, respectively) were investigated as a first step to understand their implication in hypoxia. Tributaries and Gulf contributions were compared to St. Lawrence Estuary inventories for the spring freshet (May), the summer low-flow (August), and the fall-mixing (October). Furthermore, changes in OM ratios were examined along the estuarine gradient from the upper St. Lawrence Estuary (USLE), downstream of the maximum turbidity zone, to the lower estuary (LSLE). For the USLE, net transport was always positive and net export/loading ratios suggested that 64–90% of POM and 30–63% of DOM were either retained or transformed during its course from tributaries to LSLE. Net transport from the USLE toward the LSLE was 3–13 fold more important in May than in August or October. For the LSLE, net transport to the Gulf was generally negative meaning that OM production was the dominating proces. The extremely high net export/loading ratios in August indicate that POM production was 28.8 to 41.4 times the combined inputs of tributaries and Gulf. Net export/loading ratios remained superior to one during May and October (1.7–9.4) for the LSLE. Changes along the upstream–downstream continuum were seen for POM, with a steady increase relative to total suspended matter from 7.3% to 50.2%, but they were not observed for DOM, for which no obvious trends were detected. Our results highlight the importance of explicitly considering OM in eutrophication monitoring programs of the St. Lawrence Estuary, as the mineralisation of a portion of the large OM pool size could influence our understanding of hypoxia and acidification of the deep waters of LSLE.
Impact of dynamic factors on the exchange flow between two neighboring bays with contrasting topography during summer: A numerical study
Authors: Kwak Myeong-Taek , Cho Yang-Ki
Published: January 2023

A high-resolution, three-dimensional numerical ocean model was employed to understand the exchange flow through Noryang Channel, which connects Gwangyang Bay and Jinju Bay. These two bays exhibit contrasting topographies, with Gwangyang Bay connected to the open ocean through a broad and deep channel, whereas Jinju Bay is relatively isolated from the open ocean by a narrow and shallow channel. Numerical experiments were conducted to determine the contribution of river discharge, wind stress, surface heat flux, and tides to the exchange flow between the two bays during summer. The results suggested that river discharge was the dominant factor affecting the exchange flow along Noryang Channel. Particularly, a high river discharge during summer increased the sea level in Jinju Bay, creating a barotropic flow toward Gwangyang Bay. However, the dense water entering Gwangyang Bay through the wide and deep channel generated a baroclinic flow toward Jinju Bay along the lower layer of Noryang Channel. An analytical model supported the conclusion that river discharge is the main driver of the exchange flow in Noryang Channel.
Genetic features of the marine polychaete Sirsoe methanicola from metagenomic data
Authors: Lim Shen Jean , Thompson Luke R. , Goodwin Kelly D.
Published: January 2023

The methane ice wormSirsoe methanicolais the only marine polychaete species observed to colonize the methane hydrates of the Gulf of Mexico. Methane hydrates are ephemeral features of deep-sea cold seeps, and finding worm-colonized hydrates is rare; thus, little is known about these organisms. Recent metagenomic analysis predicted prokaryotic taxa and pathways fromS. methanicolagut contents and worm fragments. Here, we increase the genetic information known aboutS. methanicolaby assembling its nuclear rRNA genes (18S rRNA and 28S rRNA), mitochondrial genome (mitogenome), and other protein-coding genes from metagenomic data. Assembled 18S rRNA and 28S rRNA gene sequences ofS. methanicolawere near-identical to previously reportedS. methanicolasequences. The 17,403-bp mitogenome ofS. methanicolais the first mitogenome sequence of the familyHesionidae, consisting of 39.03% G+C content, 13 protein-coding genes, 24 tRNAs (including two splittrnMgenes), and 2 rRNA genes. Protein-coding genes in theS. methanicolametagenomes assigned to the phylum Annelida were involved in cell adhesion, signaling, ubiquitin system, metabolism, transport, and other processes. From the metagenomes, we also found 42 homologs of the cytochrome P450 (CYP) superfamily putatively involved in polycyclic aromatic hydrocarbon (PAH) metabolism. Our results encourage further studies into the genetic adaptations ofS. methanicolato its methane hydrate habitat, especially in the context of deep-sea ecology and nutrient cycling.
Black soldier fly larvae replace traditional iced trash fish diet to enhance the delicious flavor of Chinese mitten crab (Eriocheir sinensis)
Authors: Qiu Jian-Feng , Luo Cheng , Ren Li-Hua , Li Wei , Dai Tai-Ming , Wang Guang , Sun Xiao-Ning , Moua Kou-Chang Chong , Sima Yang-Hu , Xu Shi-Qing
Published: January 2023

Chinese mitten crabs (Eriocheir sinensis) are traditionally fed iced trash fish, but the industry is facing problems such as low breeding safety. Black soldier fly (Hermetia illucens) is an alternative protein source in animal diets, including diets for aquatic animals, due to its high nutritional value. However, studies on the effects of black soldier fly on the flavor characteristics of aquatic animals are still limited. In the present study, we investigated the effects of the complete replacement of iced trash fish with black soldier fly larvae during the fattening period of Chinese mitten crab on the flavor molecule contents and evaluation indices. The levels of free amino acids and nucleotides were determined in three edible parts (muscle, hepatopancreas, and gonads) of crab. Taste activity value analysis showed that glutamic acid, glycine, alanine, and arginine were the main amino acids contributing to the umami taste and sweetness, while histidine, lysine, valine, and methionine were the main amino acids contributing to the bitterness. Equivalent umami concentration (EUC) analysis showed that female gonads had the strongest umami taste, followed by the hepatopancreas and muscle. Sweetness value (SWT) analysis showed that the sweetness of muscle was the highest. Feeding black soldier fly larvae affected the flavor characteristics of crabs with tissue and sex differences. The EUC of the female gonads and SWT of the muscle were significantly increased. Meanwhile, the EUC of the hepatopancreas and SWT of the gonads were slightly decreased in male crabs. Our results indicate that the complete replacement of iced trash fish with black soldier fly larvae during the fattening period significantly enhances the flavor characteristics of crabs based on the contents of flavoring amino acids and nucleotides. It is important for sustainable aquaculture to replace animal protein with alternative protein sources such as black soldier fly larvae.
Association of preoperative prognostic nutritional index with risk of postoperative delirium: A systematic review and meta-analysis
Authors: Hung Kuo-Chuan , Chiu Chong-Chi , Hsu Chih-Wei , Ho Chun-Ning , Ko Ching-Chung , Chen I-Wen , Sun Cheuk-Kwan
Published: January 2023

Study objective

To assess the association between prognostic nutritional index (PNI) and risk of postoperative delirium (POD) in adult patients.

Methods

MEDLINE, Google scholar, EMBASE, and Cochrane library databases were searched from inception till April 2022. The primary outcome was the association between PNI and the risk of POD, while the secondary outcomes were correlations of other prognostic factors with POD risk. The correlation between PNI and the incidence of POD was assessed with three approaches: Difference in preoperative PNI between POD and non-POD groups (Model 1) as well as the association of PNI as a continuous parameter (Model 2) or as a binary variable (i.e., low vs. high using a PNI cut-off value of 50) (Model 3) with POD risk.

Results

Analysis of nine observational studies published from 2010 to 2021 recruiting 3,743 patients showed a POD incidence of 6.4–35%. Our meta-analysis demonstrated a lower PNI among patients in the POD group (MD: −3.78, 95% CI: −4.85 to −2.71, p < 0.0001, I2 = 54.2%) compared to the non-POD group (Model 1). Pooled results revealed a negative association between PNI and POD risk for both Model 2 (OR: 0.91, 95% CI: 0.86–0.97, p = 0.002, I2 = 71%) and Model 3 (OR: 1.68, 95% CI: 1.26–2.23, p < 0.0001, I2 = 0%). Besides, while our results supported an age-dependent increase in POD risk, other factors including body-mass index, surgical time, health status, hypertension, diabetes mellitus, and male gender were non-significant predictors of POD.

Conclusion

Our results demonstrated a negative association between PNI and POD, which warrant further large-scale studies for validation.

Systematic review registration

https://www.crd.york.ac.uk/prospero/, identifier CRD42022323809.
Development and validation of risk-adjusted quality indicators for the long-term outcome of acute sepsis care in German hospitals based on health claims data
Authors: Wedekind Lisa , Fleischmann-Struzek Carolin , Rose Norman , Spoden Melissa , Günster Christian , Schlattmann Peter , Scherag André , Reinhart Konrad , Schwarzkopf Daniel
Published: January 2023

Background

Methods for assessing long-term outcome quality of acute care for sepsis are lacking. We investigated a method for measuring long-term outcome quality based on health claims data in Germany.

Materials and methods

Analyses were based on data of the largest German health insurer, covering 32% of the population. Cases (aged 15 years and older) with ICD-10-codes for severe sepsis or septic shock according to sepsis-1-definitions hospitalized in 2014 were included. Short-term outcome was assessed by 90-day mortality; long-term outcome was assessed by a composite endpoint defined by 1-year mortality or increased dependency on chronic care. Risk factors were identified by logistic regressions with backward selection. Hierarchical generalized linear models were used to correct for clustering of cases in hospitals. Predictive validity of the models was assessed by internal validation using bootstrap-sampling. Risk-standardized mortality rates (RSMR) were calculated with and without reliability adjustment and their univariate and bivariate distributions were described.

Results

Among 35,552 included patients, 53.2% died within 90 days after admission; 39.8% of 90-day survivors died within the first year or had an increased dependency on chronic care. Both risk-models showed a sufficient predictive validity regarding discrimination [AUC = 0.748 (95% CI: 0.742; 0.752) for 90-day mortality; AUC = 0.675 (95% CI: 0.665; 0.685) for the 1-year composite outcome, respectively], calibration (Brier Score of 0.203 and 0.220; calibration slope of 1.094 and 0.978), and explained variance (R2 = 0.242 and R2 = 0.111). Because of a small case-volume per hospital, applying reliability adjustment to the RSMR led to a great decrease in variability across hospitals [from median (1st quartile, 3rd quartile) 54.2% (44.3%, 65.5%) to 53.2% (50.7%, 55.9%) for 90-day mortality; from 39.2% (27.8%, 51.1%) to 39.9% (39.5%, 40.4%) for the 1-year composite endpoint]. There was no substantial correlation between the two endpoints at hospital level (observed rates: ρ = 0, p = 0.99; RSMR: ρ = 0.017, p = 0.56; reliability-adjusted RSMR: ρ = 0.067; p = 0.026).

Conclusion

Quality assurance and epidemiological surveillance of sepsis care should include indicators of long-term mortality and morbidity. Claims-based risk-adjustment models for quality indicators of acute sepsis care showed satisfactory predictive validity. To increase reliability of measurement, data sources should cover the full population and hospitals need to improve ICD-10-coding of sepsis.
Radiomics to predict the mortality of patients with rheumatoid arthritis-associated interstitial lung disease: A proof-of-concept study
Authors: Venerito Vincenzo , Manfredi Andreina , Lopalco Giuseppe , Lavista Marlea , Cassone Giulia , Scardapane Arnaldo , Sebastiani Marco , Iannone Florenzo
Published: January 2023

Objectives

Patients with rheumatoid arthritis (RA) and interstitial lung disease (ILD) have increased mortality compared to the general population and factors capable of predicting RA-ILD long-term clinical outcomes are lacking. In oncology, radiomics allows the quantification of tumour phenotype by analysing the characteristics of medical images. Using specific software, it is possible to segment organs on high-resolution computed tomography (HRCT) images and extract many features that may uncover disease characteristics that are not detected by the naked eye. We aimed to investigate whether features from whole lung radiomic analysis of HRCT may alone predict mortality in RA-ILD patients.

Methods

High-resolution computed tomographies of RA patients from January 2012 to March 2022 were analyzed. The time between the first available HRCT and the last follow-up visit or ILD-related death was recorded. We performed a volumetric analysis in 3D Slicer, automatically segmenting the whole lungs and trachea via the Lung CT Analyzer. A LASSO-Cox model was carried out by considering ILD-related death as the outcome variable and extracting radiomic features as exposure variables.

Results

We retrieved the HRCTs of 30 RA-ILD patients. The median survival time (interquartile range) was 48 months (36–120 months). Thirteen out of 30 (43.33%) patients died during the observation period. Whole line segmentation was fast and reliable. The model included either the median grey level intensity within the whole lung segmentation [high-resolution (HR) 9.35, 95% CI 1.56–55.86] as a positive predictor of death and the 10th percentile of the number of included voxels (HR 0.20, 95% CI 0.05–0.84), the voxel-based pre-processing information (HR 0.23, 95% CI 0.06–0.82) and the flatness (HR 0.42, 95% CI 0.18–0.98), negatively correlating to mortality. The correlation of grey level values to their respective voxels (HR 1.52 95% CI 0.82–2.83) was also retained as a confounder.

Conclusion

Radiomic analysis may predict RA-ILD patients’ mortality and may promote HRCT as a digital biomarker regardless of the clinical characteristics of the disease.
Targeted thorium-227 conjugates as treatment options in oncology
Authors: Karlsson Jenny , Schatz Christoph A. , Wengner Antje M. , Hammer Stefanie , Scholz Arne , Cuthbertson Alan , Wagner Volker , Hennekes Hartwig , Jardine Vicki , Hagemann Urs B.
Published: January 2023

Targeted alpha therapy (TAT) is a promising approach for addressing unmet needs in oncology. Inherent properties make α-emitting radionuclides well suited to cancer therapy, including high linear energy transfer (LET), penetration range of 2–10 cell layers, induction of complex double-stranded DNA breaks, and immune-stimulatory effects. Several alpha radionuclides, including radium-223 (223Ra), actinium-225 (225Ac), and thorium-227 (227Th), have been investigated. Conjugation of tumor targeting modalities, such as antibodies and small molecules, with a chelator moiety and subsequent radiolabeling with α-emitters enables specific delivery of cytotoxic payloads to different tumor types. 223Ra dichloride, approved for the treatment of patients with metastatic castration-resistant prostate cancer (mCRPC) with bone-metastatic disease and no visceral metastasis, is the only approved and commercialized alpha therapy. However, 223Ra dichloride cannot currently be complexed to targeting moieties. In contrast to 223Ra, 227Th may be readily chelated, which allows radiolabeling of tumor targeting moieties to produce targeted thorium conjugates (TTCs), facilitating delivery to a broad range of tumors. TTCs have shown promise in pre-clinical studies across a range of tumor-cell expressing antigens. A clinical study in hematological malignancy targeting CD22 has demonstrated early signs of activity. Furthermore, pre-clinical studies show additive or synergistic effects when TTCs are combined with established anti-cancer therapies, for example androgen receptor inhibitors (ARI), DNA damage response inhibitors such as poly (ADP)-ribose polymerase inhibitors or ataxia telangiectasia and Rad3-related kinase inhibitors, as well as immune checkpoint inhibitors.
Using metabolic potential within the airway microbiome as predictors of clinical state in persons with cystic fibrosis
Authors: Shumyatsky Gabriella , Burrell Aszia , Chaney Hollis , Sami Iman , Koumbourlis Anastassios C. , Freishtat Robert J. , Crandall Keith A. , Zemanick Edith T. , Hahn Andrea
Published: January 2023

Introduction

Pulmonary exacerbations (PEx) in persons with cystic fibrosis (CF) are primarily related to acute or chronic inflammation associated with bacterial lung infections, which may be caused by several bacteria that activate similar bacterial genes and produce similar by-products. The goal of our study was to perform a stratified functional analysis of bacterial genes at three distinct time points in the treatment of a PEx in order to determine the role that specific airway microbiome community members may play within each clinical state (i.e., PEx, end of antibiotic treatment, and follow-up). Our secondary goal was to compare the change between clinical states with the metabolic activity of specific airway microbiome community members.

Methods

This was a prospective observational study of persons with CF treated with intravenous antibiotics for PEx between 2016 and 2020 at Children’s National Hospital. Demographic and clinical information as well as respiratory samples were collected at hospital admission for PEx, end of antibiotic treatment, and follow-up. Metagenomic sequencing was performed; MetaPhlAn3 and HUMANn3 were used to assign sequences to bacterial species and bacterial metabolic genes, respectively.

Results

Twenty-two persons with CF, with a mean age of 14.5 (range 7–23) years, experienced 45 PEx during the study period. Two-hundred twenty-one bacterial species were identified in the respiratory samples from the study cohort. Ten bacterial species had differential gene abundance across changes in the clinical state including Staphylococcus aureus, Streptococcus salivarius, and Veillonella atypica (all padj < 0.01 and log2FoldChange > |2|). These corresponded to a differential abundance of bacterial genes, with S. aureus accounting for 81% of the genes more abundant in PEx and S. salivarius accounting for 83% of the genes more abundant in follow-up, all compared to the end of treatment. Lastly, 8,653 metabolic pathways were identified across samples, with again S. aureus and S. salivarius contributing to the differential abundance of pathways (106 in PEx vs. 66 in follow-up, respectively). V. atypica was associated with a single metabolic pathway (UDP-N-acetyl-D-glucosamine biosynthesis) increased in follow-up compared to PEx.

Discussion

Taken together, these data suggest that the metabolic potential of bacterial species can provide more insight into changes across clinical states than the relative abundance of the bacteria alone.
The impact of COVID-19 on kidney transplant care
Authors: Zhang Chi , Kodali Lavanya , Mour Girish , Jadlowiec Caroline , Mathur Amit K.
Published: January 2023

The SARS-CoV-2 virus precipitated the coronavirus 2019 (COVID-19) pandemic, which placed considerable strain on healthcare systems and necessitated immediate and rapid alterations in the delivery of healthcare. In the transplant population, COVID-19 directly impacts an inherently vulnerable population in the setting of immunosuppression and co-morbidities, but also further complicates the clinical evaluation and management of kidney transplant candidates and recipients in a strained healthcare environment being challenged by the pandemic. Many transplant centers around the world saw mortality rate spikes in organ recipients related to COVID-19, and changes in care delivery abound. This review evaluates the care of the kidney transplant patient through all phases of the process including pre-operative evaluations, perioperative care, post-transplantation considerations, and how the global pandemic has changed the way we care for our patients.
Acupressure versus parecoxib sodium in acute renal colic: A prospective cohort study
Authors: Chen Chiwei , Zhang Zhenpeng , Lin Mandi , Wang Zhigang , Liu Hao , Meng Hao , Wang Jun , Chen Ming , Xiang Songtao , Qiu Yunqiao , Liu Hong
Published: January 2023

Background

Here provides a complementary treatment, acupressure at the Qiu acupoint, a novel acupoint, which potentially alleviates renal colic.

Materials and methods

90 patients were included in this study. Acupressure-group patients (n = 46) were administered acupressure at the Qiu acupoint following a preset protocol. Parecoxib sodium-group patients (n = 44) were administered parecoxib sodium (40 mg) (via the direct intravenous route). The visual analog scale (VAS) was used to evaluate pain intensity at baseline and at 1, 5, 10, 20, 30, and 120 min after initiating the intervention. Linear mixed effects model was performed to detect the rate of decrease of VAS per time and their covariant effect on the efficacy of acupressure.

Results

No significant statistical differences in baseline data and VAS scores were observed. The acupressure group obtained lower VAS scores at the 1st, 5th, 10th, and 20th minute than the parecoxib sodium group after initiating the intervention (mean: 4.33 vs. 7.61, mean difference (MD): 3.29, 95% CI: 0.23, 2.84; mean: 2.65 vs. 7.61, MD: 4.96, 95% CI: 4.44, 5.49; mean: 1.63 vs. 6.59, MD: 4.96, 95% CI: 4.48, 5.44; mean: 1.26 vs. 3.64 MD: 2.38, 95% CI: 1.87, 2.88; P < 0.05). The markedly effective rate was similar between the two groups. The linear mixed effects model demonstrated that acupressure at the Qiu point was significantly faster than parecoxib sodium in decreasing VAS scores with an estimate of –2.05 (95% CI: –2.51, –1.59, p = 0.000), especially within 10 minutes with an estimate of 0.18 (95% CI: 0.12, 0.25, p = 0.000).

Conclusion

Acupressure at the Qiu acupoint is significantly faster than parecoxib sodium in decreasing VAS scores within 10 minutes.

Clinical trial registration

http://www.chictr.org.cn/, identifier 2100047168.
Renal replacement therapy in sarcoidosis
Authors: Calatroni Marta , Moroni Gabriella , Ponticelli Claudio
Published: January 2023

Sarcoidosis is a systemic inflammatory disease of unknown etiology. Kidney involvement in sarcoidosis may be present in up 25–30% of cases. An early diagnosis and prompt treatment with corticosteroids can improve the prognosis but rarely renal sarcoidosis can lead to kidney failure needing renal replacement therapy (RRT). Acute kidney injury (AKI) in sarcoidosis may be caused by granulomatous interstitial nephritis (GIN) or hypercalcemia. These disorders are usually clinically silent and may lead end stage renal disease (ESKD) if not diagnosed or detected too late. In patients with ESKD, dialysis and renal transplantation can offer results comparable to those observed in patients with other causes of kidney failure. Based on a review of literature, we present an overview of RRT in patients with AKI or chronic kidney disease (CKD) caused by sarcoidosis.
Global trends and hotspots of phage therapy for bacterial infection: A bibliometric visualized analysis from 2001 to 2021
Authors: Maimaiti Zulipikaer , Li Zhuo , Xu Chi , Chen Jiying , Chai Wei
Published: January 2023

Background

Antibiotic resistance is one of the main global threats to human health, and just the development of new antimicrobial medications is not enough to solve the crisis. Phage therapy (PT), a safe and effective treatment method, has reignited the interest of researchers due to its efficacy in the clinical treatment of drug-resistant bacterial infections. There is, however, no bibliometric analysis of the overall trends on this topic. Therefore, this study aims to provide an overview of the current state of development and research in this area.

Methods

We extracted all relevant publications from the Web of Science Core Collection (WoSCC) database between 2001 and 2021. We performed bibliometric analysis and visualization using CiteSpace, VOS viewer, and R software. Annual trends of publications, countries/regions distributions, institutions, funding agencies, co-cited journals, author contributions, core journals, references, and keywords were analyzed.

Results

A total of 6,538 papers were enrolled in this study, including 5,364 articles and 1,174 reviews. Publications have increased drastically from 61 in 2001 to 937 in 2021, with 3,659 articles published in the last 5 years. North America, Western Europe, and East Asia were significant contributor regions. The United States, China, and the United Kingdom were the most productive countries. The Polish Academy of Sciences was the most contributive institution. Frontiers in Microbiology and Applied and Environmental Microbiology were the most productive and co-cited journals. A. Gorski and R. Lavigne published most articles in this field, while V. A. Fischetti was the author with the most cited. Regarding keywords, research focuses include phage biology, phage against clinically important pathogens, phage lysis proteins, phage therapy, biofilm-related research, and recent clinical applications.

Conclusion

Phage therapy is a potential strategy for combating antibiotic resistance, and it will provide us with an alternative therapeutic option for bacterial infection. According to global trends, the scientific output of PT in bacterial infections is increasing, with developed countries such as the United States leading the way in this area. Although the safety and efficacy of PT have been proven, more clinical trials on the phages against infectious diseases caused by various pathogens are still needed.
Into the darkness of the microbial dark matter in situ activities through expression profiles of Patescibacteria populations
Authors: Vigneron Adrien , Cruaud Perrine , Guyoneaud Rémy , Goñi-Urriza Marisol
Published: January 2023

Patescibacteria form a highly diverse and widespread superphylum of uncultured microorganisms representing a third of the global microbial diversity. Most of our knowledge on Patescibacteria putative physiology relies on metagenomic mining and metagenome-assembled genomes, but the in situ activities and the ecophysiology of these microorganisms have been rarely explored, leaving the role of Patescibacteria in ecosystems elusive. Using a genome-centric metatranscriptomic approach, we analyzed the diel and seasonal gene transcription profiles of 18 Patescibacteria populations in brackish microbial mats to test whether our understanding of Patescibacteria metabolism allows the extrapolation of their in situ activities. Although our results revealed a circadian cycle in Patescibacteria activities, a strong streamlined genetic expression characterized the Patescibacteria populations. This result has a major consequence for the extrapolation of their physiology and environmental function since most transcribed genes were uncharacterized, indicating that the ecophysiology of Patescibacteria cannot be yet reliably predicted from genomic data.
Applying fulvic acid for sediment metals remediation: Mechanism, factors, and prospect
Authors: Song Chuxuan , Sun Shiquan , Wang Jinting , Gao Yang , Yu Guanlong , Li Yifu , Liu Zhengqian , Zhang Wei , Zhou Lean
Published: January 2023

Fulvic acid (FA) has been shown to play a decisive role in controlling the environmental geochemical behavior of metals. As a green and natural microbial metabolite, FA is widely used in environmental remediation because of its good adsorption complexation and redox ability. This paper introduces the reaction mechanism and properties of FA with metals, and reviews the progress of research on the remediation of metal pollutant by FA through physicochemical remediation and bioremediation. FA can control the biotoxicity and migration ability of some metals, such as Pb, Cr, Hg, Cd, and As, through adsorption complexation and redox reactions. The concentration, molecular weight, and source are the main factors that determine the remediation ability of FA. In addition, the ambient pH, temperature, metal ion concentrations, and competing components in sediment environments have significant effects on the extent and rate of a reaction between metals and FA during the remediation process. Finally, we summarize the challenges that this promising environmental remediation tool may face. The research directions of FA in the field of metals ecological remediation are also prospected. This review can provide new ideas and directions for the research of remediation of metals contaminants in sediments.
Sauchinone alleviates dextran sulfate sodium-induced ulcerative colitis via NAD(P)H dehydrogenase [quinone] 1/NF-kB pathway and gut microbiota
Authors: Wu Kun , Liu Xianjun , Meng Xianglong , Cao Lingling , Li Hao , Bi Yingxin , Wang Mengyuan , Wang Mingchuan , Jiang Yang
Published: January 2023

Objective

This study evaluated the effects of sauchinone on dextran sulfate sodium (DSS)-induced ulcerative colitis (UC) mice model and investigated the underlying mechanisms of the downstream pathway and gut microbiota.

Methods

The UC mice model was induced by DSS. The disease phenotypes were determined through pathological symptoms (body weight and disease activity index score), inflammation markers (histological and inflammatory factor detections), and colonic mucosal barrier damage (detection of tight junction proteins). The level of the NF-κB pathway was detected through marker proteins. Database and bioinformatics analyses were used to predict sauchinone-mediated downstream molecules that were previously identified by expression analysis. Mouse feces were collected to detect the V3–V4 region of the 16S rRNA gene.

Results

In DSS-induced UC mice, sauchinone alleviated pathological symptoms, inhibited inflammation, and prevented mucosal barrier damage. Sauchinone further inhibited the NF-κB pathway by upregulating NAD (P) H dehydrogenase [quinone] 1 (NQO1) in DSS-induced UC mice. Moreover, sauchinone regulated the diversity and composition of the gut microbiota in mice, stimulating the growth of Firmicutes and inhibiting the growth of Proteobacteria and Bacteroidetes.

Conclusion

Therefore, sauchinone exerted therapeutic effects on UC in mice by regulating the NQO1/NF-κB pathway and altering the gut microbiota. This provides a theoretical basis for developing sauchinone as a therapeutic agent and extends our understanding of its bioactivity.
Tumor microenvironment and epithelial-mesenchymal transition in bladder cancer: Cytokines in the game?
Authors: Martins-Lima Cláudia , Chianese Ugo , Benedetti Rosaria , Altucci Lucia , Jerónimo Carmen , Correia Margareta P.
Published: January 2023

Bladder cancer (BlCa) is a highly immunogenic cancer. Bacillus Calmette-Guérin (BCG) is the standard treatment for non-muscle invasive bladder cancer (NMIBC) patients and, recently, second-line immunotherapies have arisen to treat metastatic BlCa patients. Understanding the interactions between tumor cells, immune cells and soluble factors in bladder tumor microenvironment (TME) is crucial. Cytokines and chemokines released in the TME have a dual role, since they can exhibit both a pro-inflammatory and anti-inflammatory potential, driving infiltration and inflammation, and also promoting evasion of immune system and pro-tumoral effects. In BlCa disease, 70–80% are non-muscle invasive bladder cancer, while 20–30% are muscle-invasive bladder cancer (MIBC) at the time of diagnosis. However, during the follow up, about half of treated NMIBC patients recur once or more, with 5–25% progressing to muscle-invasive bladder cancer, which represents a significant concern to the clinic. Epithelial-mesenchymal transition (EMT) is one biological process associated with tumor progression. Specific cytokines present in bladder TME have been related with signaling pathways activation and EMT-related molecules regulation. In this review, we summarized the immune landscape in BlCa TME, along with the most relevant cytokines and their putative role in driving EMT processes, tumor progression, invasion, migration and metastasis formation.
Clinical study on endovascular recanalization of non-acute symptomatic middle cerebral artery occlusion
Authors: Xia Jinchao , Li Hao , Zhang Kun , Wang Ziliang , Li Tianxiao
Published: January 2023

Objective

Endovascular recanalization in patients with non-acute symptomatic middle cerebral artery occlusion remains clinically challenging. Here, we aimed to evaluate the feasibility and safety of endovascular recanalization for non-acute symptomatic middle cerebral artery occlusion and propose a new patient classification.

Methods

Between January 2019 and December 2021, 88 patients with non-acute symptomatic middle cerebral artery occlusion underwent prospective endovascular recanalization at our hospital. All patients were divided into three groups according to occlusion length, occlusion duration, occlusion nature, calcification of the occlusion site, and occlusion angulation. The indicators of each group were analyzed, including general baseline data, imaging data, surgical conditions, and follow-up results.

Results

Of the 88 patients, 73 were successfully recanalized and 15 were abandoned because the instruments either could not reach the distal true lumen of the occlusion or broke through the blood vessels. The overall technical success rate was 83.0% (73/88), and perioperative complications occurred in 15 patients. Preoperatively, all patients were divided into three risk groups: low, medium, and high. From the low- to high-risk groups, the recanalization rate gradually decreased (100.0, 91.7, and 16.7%, respectively, P = 0.020), the perioperative complication rate gradually increased (0, 13.9, and 83.3%, respectively, P < 0.001), the proportion of the modified Rankin scale scores >2 at 90 days increased (0, 11.7, and 50.0%, P < 0.001), and the restenosis/reocclusion rates in the 73 cases of successful recanalization increased (0, 16.1, and 100%, P = 0.012) during follow-up.

Conclusion

Endovascular recanalization may be feasible and safe in well-selected patients with non-acute symptomatic middle cerebral artery occlusion, especially in the low- and medium-risk groups.
Acupuncture for neuropathic pain: A meta-analysis of randomized control trials
Authors: Feng Zitong , Cui Shaoyang , Yang Huijun , Wang Yixiao , Zhou Xuan , Wong John , Lai Liting , Yang Zeyu , Huang Bingjing , Zheng Huiyan , Xu Mingzhu
Published: January 2023

Background

Neuropathic pain (NP) is expected to increase due to the high risk of global population aging. Acupuncture has a definite clinical effect on NP. Therefore, a systematic review and meta-analysis were conducted to evaluate the effect on pain intensity and safety of acupuncture in patients with NP.

Methods

An encompassing search of specific authoritative databases in English, from their inception to 2022, was performed. The databases were as follows: Scopus, Ovid EMBASE, Ovid Cochrane Database of Systematic Reviews, Ovid Cochrane Central Register of Controlled Trials, Ovid MEDLINE(R) and Epub Ahead of Print, In-Process and Other Non-Indexed Citations, and Daily. All the randomized controlled trials regarding the acupuncture treatment of NP will be included. Methodological quality assessment of the included trials was assessed based on the risk of bias from the Cochrane handbook. A meta-analysis was performed for the main outcomes. In addition, sensitivity analysis, subgroup analysis, and funnel plot were also carried out.

Results

A total of 16 studies with 1,021 patients with NP were evaluated in a systematic review. According to the results of the overall meta-analysis in eight RCTs with 338 participants, the acupuncture group was better than the control group in improving changes in pain intensity (SMD −0.59, 95% CI: −0.95 to −0.23, P = 0.001). In subgroup analysis, five trials indicated that acupuncture was more effective in improving changes in pain intensity than sham acupuncture (SMD −0.54, 95% CI: −0.95 to −0.13, P = 0.01), two trials evaluated the effect on changes in pain intensity in the comparison of acupuncture and conventional treatments, no significant difference existed (SMD −0.61, 95% CI: −1.83 to 0.61, P = 0.33), and one trial compared acupuncture with blank control evaluating the effect of changes in pain intensity with a significant difference. Eleven studies mentioned the safety conditions and acupuncture-induced AEs were mild and reversible. Both the sensitivity analysis and funnel plot analysis showed that the meta-analysis was stable and irreversible without publication bias. The GRADE was rated as “very low.”

Conclusion

The acupuncture group had higher effectiveness than sham intervention or blank control for changes in pain intensity, but there is no significant difference between acupuncture and conventional treatments in treating NP. The acupuncture-induced adverse events were mild and reversible. However, the interpretation of our results should be performed cautiously due to the low methodological quality of selected publications.

Systematic review registration

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022306461.