Tag: LEfse

Author Contributions Conceptualization, Y.Y. and Y.G.; Data curation, M.L. and W.Z.; Formal analysis, M.L., W.Z., W.T. and J.L.; Funding acquisition, Y.Y. and Y.G.; Investigation, J.X., Y.Y. and Y.G.; Methodology, M.L., J.L. and Y.Y.; Project administration, Y.Y.; Resources, J.X., Y.Y. and Y.G.; Software, M.L., W.Z. and W.T.; Supervision, J.X., Y.Y. and…

Patient demographics Among the children, 102 were diagnosed with ARFID, and 33 were healthy. There were 50 males and 52 females in the ARFID group and 15 males and 18 females in the healthy control group (HC group). There was no significant difference in age (P = 0.352) or sex composition (P = 0.512)….

Characteristics of participants and analyses A total of 115 individuals (43 PDD, 45 PD-MCI) and 27 HC were included in this study. Both 16 S rRNA gene amplicon sequencing based microbiome analysis and metaproteomics profiling were performed for all salivary samples collected from the participants (Fig. 1). Fig. 1: Experimental overview….

Female Asmt ft/ft mice exhibits anxiety- and depression-like behaviors We first examined the anxiety- and depression-like behaviors in mice. Our results showed that female Asmtft/ft mice had less distance in center (p < 0.001) and a smaller number of poking (p < 0.05) in the open field test (OFT, Fig. 1a–c). In the forced swim…

Introduction The microbiomes of different host organisms are currently described by using culture-independent sequencing methods (Harvey & Holmes, 2022). Shotgun metagenomic and 16S rDNA sequencing methods are commonly used to identify the taxonomic composition of microbial communities in several studies (de Melo et al., 2020; Mackelprang et al., 2011; Monaco…

A flow diagram of the study is shown in Fig. 3. Figure 3 Flow diagram of the study. Ethical approval and consent to participant This study was approved by the Institutional Review Board of the Nagoya University Graduate School of Medicine (approval number 2022-0084; approval date, June 3, 2022). Written informed…

Introduction Diabetes is a growing public health problem with increasing prevalence and mortality that threatens the health of people globally.1 In 2021, the global prevalence of diabetes in adults aged 20 to 79 years was estimated at 537 million, mainly caused by type 2 diabetes, and the number is expected…

. 2023 Sep 18:14:1197418. doi: 10.3389/fphar.2023.1197418. eCollection 2023. Affiliations Expand Affiliation 1 Chongqing Three Gorges Medical College, Chongqing Key Laboratory of Development and Utilization of Genuine Medicinal Materials in Three Gorges Reservoir Area, Chongqing, China. Free PMC article Item in Clipboard Wei Xiong et al. Front Pharmacol. 2023. Free PMC article…

Dynamics of immunogenicity at 6 months after BNT162b2 and CoronaVac vaccination From April 2021 to March 2022, we longitudinally followed 161 COVID-19 vaccinees who had received BNT162b2 (N = 121, 65.3% females) or CoronaVac vaccines (N = 40, 72.5% females). BNT162b2 vaccinees were younger compared to CoronaVac vaccinees [median (IQR) in years: 42 (29,…

Trillions of microbes colonize the human body and play critical roles in multiple fundamental physiological processes. Changes in microbial composition and functions are intimately interwoven with various diseases, ranging from obesity to cancer and autism [1,2]. With the rapid development of sequencing technologies, projects such as the Human Microbiome Project…

Introduction Allergic airway diseases affect many people worldwide, and incidences are still increasing gradually. Allergic rhinitis and allergic asthma, are typical chronic nasopharyngitis respiratory diseases in pediatric, causing an enormous burden of illness and high economic costs to the community.1 Allergic rhinitis and allergic asthma are immunoglobulin E (IgE)-mediated inflammatory…

Species of intestinal protozoan parasites The parasites identified using metagenomics belonged to the genera Giardia, Eimeria, Cryptosporidium, Blastocystisand Entamoeba (Fig. 1A). Specific genetic information is shown in Additional file 3 : Table S2. Not all positive samples were successfully amplified. Based on these results, the parasite species were in calves…

Species of intestinal protozoan parasites The parasites identified using metagenomics belonged to the genera Giardia, Eimeria, Cryptosporidium, Blastocystis, and Entamoeba (Fig. 1A). Specific genetic information is shown in Additional file 3: Table S2. Not all positive samples were successfully amplified. Based on these results, the parasite species in calves were G….

Clinical factors associated with outgrowth of CMA To determine environmental and clinical factors associated with outgrowth of CMA in our data set, we performed statistical tests (two-sided Mann–Whitney U-test for numeric variables, Fisher’s exact test for binary variables) to the metadata of the subjects used in this study (clinical characteristics,…

Comment: Building Multifactor Model in DESeq2 by Abhishek Singh &utrif; 20 The question has been updated, I do not understand how it is nested? and if it is then how can I fix it? Comment: Building Multifactor Model in DESeq2 by ATpoint &starf; 3.1k It means any of two or…

Psyllid sampling, tissue collection and DNA isolation Adult D. citri newly emerged (five days old) was initially harvested from Citrus Tachibana uninfected CLas in 2020 at Guangxi province, China, and was successively reared on Murraya paniculata at Guangxi Special Crops Research Institute for more than 15 generations. All cages and…

The clinical and physical variables Table 1 presents the general characteristics of the 106 included participants. The mean age was approximately 36 years in both healthy and MAFLD groups. Of the 106 participants, 81 (68 men, 13 women) were in the MAFLD group. Body mass index (BMI) level was significantly lower…

Ahemad M, Khan MS (2012) Effect of fungicides on plant growth promoting activities of phosphate solubilizing Pseudomonas putida isolated from mustard (Brassica compestris) rhizosphere. Chemosphere 86(9):945–950. doi.org/10.1016/j.chemosphere.2011.11.013 Article  CAS  PubMed  Google Scholar  Al-Askar AA, Saber WI, Ghoneem KM, Hafez EE, Ibrahim AA (2021) Crude citric acid of Trichoderma asperellum: tomato…

Structure of the macrofouling/steel interface Soft-fouling and hard-fouling organisms all could pose potential threats to marine facilities. Oysters, as representatives of hard-fouling organisms, are composed of a soft body protected by two complex shell sections. The oyster shell is primarily made of 97% calcium carbonate, which provides it with significant…

Background The prevalence of type 2 diabetes (T2D) is rapidly increasing worldwide, with an estimated global prevalence of approximately 552 million by 2030.1 Long-term hyperglycemia in T2D patients can lead to vascular endothelial damage, which includes microvascular disease such as diabetic retinopathy and nephropathy, neuropathy, and macrovascular disease including peripheral…

Introduction Hyperuricemia is a disease caused by irregular purine metabolism, which is always accompanied by excessive production or abnormal excretion of uric acid (UA).1 Most notably, the overall incidence of hyperuricemia in China has been increasing over the past decade with the westernization of eating habits.2,3 However, there are blind…

Introduction Tea trees (Camellia sinensis (L.) O. Kuntze) are among the most important economic trees in the world, as an important economic crop, which is widely planted in acidic soil in the tropical and sub-tropical zones of China (Liu et al. Citation2019). Meanwhile, tea is an aluminium (Al) accumulating plant that…

Acquired MEC is a common condition in the field of otolaryngology. Therefore, the subjects included in this study were all acquired MEC. Bacterial infections play an important role in the onset and development of acquired MEC, and microbial communities play an indispensable role in all ecosystems, particularly living organisms (Lemanceau…

All experimental procedures were conducted at the University of Illinois at Urbana-Champaign and followed protocols approved by the Institutional Animal Care and Use Committee (IACUC) at the University of Illinois at Urbana-Champaign under protocol number 17172. All ARRIVE, and IACUC guidelines and regulations were followed during the entire duration of…

1. Introduction Fusarium fungi are world-wide producers of a range of mycotoxins. Deoxynivalenol (DON) belonging to the group B trichothecenes, is one of the most prevalent food-associated mycotoxins mainly produced by Fusarium graminearum and Fusarium culmorum, and frequently contaminates cereals and cereal products [1,2]. Almost half of a total of…

Human ethics statement This study was approved by the Human Ethical Review Committee of Khon Kaen University, Thailand (HE641434) following the principles of the Declaration of Helsinki. Before stool samples were collected, participants were required to complete and sign written informed-consent forms. Participants and samples All samples came from residents…

Introduction An intra-abdominal abscess is a collection of pus or infected fluid located inside or near the liver, kidneys, pancreas, spleen, or other abdominal organs.1 Unlike skin abscesses with obvious signs of redness and swelling,2 intra-abdominal abscesses occur less frequently and are often difficult to identify, of which patients may…

This prospective observational study (NCT04803695) complied with the Declaration of Helsinki (current version, Fortaleza, Brazil, October 2013). Our institution’s Internal Review Board approved the study, and all patients gave their written informed consent (No. HCB/2018/0236, Hospital Clinic Barcelona). Sputum samples and DNA extraction Thirty-three sputum samples were collected from patients…

Background: Psoriasis is an inflammatory skin disease. The correlation between intestinal microbiota and immune-mediated diseases makes scientists pay attention to the pathogenic role of microbiota. Objective: The aim of this study was to identify the gut microbial composition of patients with psoriasis. Methods: 16S rRNA gene sequencing method was used…

excluded in the analysis. Solve optimization problems using an R interface to NLopt. The overall false discovery rate is controlled by the mdFDR methodology we In this formula, other covariates could potentially be included to adjust for confounding. depends on our research goals. W, a data.frame of test statistics. enter…

Ethics statement All animal experiments were performed in compliance with the Regulations for the Care and Use of Laboratory Animals issued by the Ministry of Science and Technology of the People’s Republic of China, which enforces the ethical use of animals. The protocol was approved by Institutional Animal Care and…

Recent medical interests have focused on the gut microbiome as the epicenter of health. Indeed, the microbiota-gut-brain axis has been proven to influence mental and physical wellbeing. Meditation, the internal mental exercise of paying attention to the present moment, can also impact one’s physical and mental health. However, there has…

General description of sequences After the quality filtering step, removal of chimeric fragments, and read merging, a total of 3,378,323 reads with 3007 different features was obtained, with an average of 27,244 sequences per individual sample. After quality filtering, none of the samples was excluded from the analysis of microbial…

The bioBakery help forum Sign Up Log In Log In Popular Announcing MetaPhlAn 4MetaPhlAn Announcing HUMAnN 3.5HUMAnN Clear guidance needed for comparing across samples with varying sequencing depthMetaPhlAn List of taxa in Metaphlan4 databaseMetaPhlAn Metaphlan 4 install issueMetaPhlAn ERROR: The MetaPhlAn2 taxonomic profile provided was not generated with the database…

Distribution of nitrogen-cycling pathways in groundwater Differences in nitrogen-cycling processes based on oxygen and nitrate concentrations Sixteen metagenomes (Table S4) were obtained from duplicate wells at four sites (A–D) from two unconfined alluvial aquifers (Canterbury, Fig. S1). These sites encompassed varied nitrate (0.45–12.6 g/m3), DO (0.37–7.5 mg/L), and dissolved organic carbon (DOC) (0–26 g/m3)…